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IndexError: sequence length is not enough in R1 read #285

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calcaidecabello opened this issue May 14, 2024 · 7 comments
Open

IndexError: sequence length is not enough in R1 read #285

calcaidecabello opened this issue May 14, 2024 · 7 comments

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@calcaidecabello
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Hi,

I am trying to run celescope. I built the reference genome and I have created the shell scripts, but I obtain this error:

sh Bnsortednuclei1.sh
2024-05-14 14:13:14,148 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', outdir='.//Bnsortednuclei1/00.sample', sample='Bnsortednuclei1', thread='16', debug=False, fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', chemistry='auto', wells=384, func=<function sample at 0x7fa2b78e0820>)
2024-05-14 14:13:14,209 - celescope.tools.sample.run - INFO - start...
2024-05-14 14:13:14,872 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:13:14,872 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:13:14,872 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 68, in sample
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 36, in run
chemistry = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', chemistry='auto', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='', SAM_attributes='', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', fq2='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz', outdir='.//Bnsortednuclei1/01.starsolo', sample='Bnsortednuclei1', thread='16', debug=False, func=<function starsolo at 0x7fc688421ee0>)
2024-05-14 14:13:21,219 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:13:21,220 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:13:21,220 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 185, in starsolo
with Starsolo(args) as runner:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 41, in init
chemistry_list = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
2024-05-14 14:13:26,722 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7fc0797f64c0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7fc0797f64c0>)
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in init
self.adata = sc.read_10x_mtx(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
return _read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file Bnsortednuclei1/outs/filtered/matrix.mtx.gz.
(Cris_singleron_snseq) calcaide@dell-node-4:/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/shell$ cd ../
(Cris_singleron_snseq) calcaide@dell-node-4:/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460$ sh ./shell/Bnsortednuclei1.sh
2024-05-14 14:20:03,762 - celescope.tools.sample.sample - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', outdir='.//Bnsortednuclei1/00.sample', sample='Bnsortednuclei1', thread='16', debug=False, fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', chemistry='auto', wells=384, func=<function sample at 0x7fe755b11820>)
2024-05-14 14:20:03,835 - celescope.tools.sample.run - INFO - start...
2024-05-14 14:20:04,488 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:20:04,489 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:20:04,489 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 68, in sample
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/sample.py", line 36, in run
chemistry = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', chemistry='auto', pattern=None, whitelist=None, adapter_3p='AAAAAAAAAAAA', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', outFilterMatchNmin='50', soloCellFilter='EmptyDrops_CR 3000 0.99 10 45000 90000 500 0.01 20000 0.001 10000', starMem='32', STAR_param='', SAM_attributes='', soloFeatures='Gene GeneFull_Ex50pAS', fq1='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz', fq2='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R2.fastq.gz', outdir='.//Bnsortednuclei1/01.starsolo', sample='Bnsortednuclei1', thread='16', debug=False, func=<function starsolo at 0x7fb7396a1ee0>)
2024-05-14 14:20:10,529 - celescope.tools.barcode.check_chemistry - INFO - start...
2024-05-14 14:20:10,530 - celescope.tools.barcode.check_chemistry - INFO - /netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/00_rawdata/Bnsortednuclei_R1.fastq.gz
2024-05-14 14:20:10,530 - celescope.tools.barcode.get_chemistry - INFO - start...
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 185, in starsolo
with Starsolo(args) as runner:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/starsolo.py", line 41, in init
chemistry_list = ch.check_chemistry()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 56, in check_chemistry
chemistry = self.get_chemistry(fastq1)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 131, in get_chemistry
chemistry = self.seq_chemistry(seq)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 87, in seq_chemistry
linker_flv_rna = Barcode.get_seq_str(seq, self.pattern_dict_flv_rna["L"])
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/barcode.py", line 276, in get_seq_str
raise IndexError(f"sequence length is not enough in R1 read: {seq}")
IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT
2024-05-14 14:20:15,806 - celescope.rna.analysis.analysis - INFO - start...
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f3cca87e4c0>)
CeleScope version: 2.0.7 Args: Namespace(subparser_assay='rna', genomeDir='/netscratch/dep_coupland/grp_turck/People/Cristina/GC_6460/ZS11/', matrix_file='.//Bnsortednuclei1/outs/filtered', outdir='.//Bnsortednuclei1/02.analysis', sample='Bnsortednuclei1', thread='16', debug=False, func=<function analysis at 0x7f3cca87e4c0>)
Traceback (most recent call last):
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/bin/celescope", line 8, in
sys.exit(main())
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main
args.func(args)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/utils.py", line 45, in wrapper
result = func(*args, **kwargs)
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 64, in analysis
runner.run()
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/rna/analysis.py", line 38, in run
with analysis_wrapper.Scanpy_wrapper(self.args, display_title=self.display_title) as scanpy_wrapper:
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/celescope/tools/analysis_wrapper.py", line 59, in init
self.adata = sc.read_10x_mtx(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 490, in read_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 554, in _read_v3_10x_mtx
adata = read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 112, in read
return _read(
File "/netscratch/dep_coupland/grp_turck/lib/micromamba/envs/Cris_singleron_snseq/lib/python3.9/site-packages/scanpy/readwrite.py", line 737, in _read
raise FileNotFoundError(f'Did not find file {filename}.')
FileNotFoundError: Did not find file Bnsortednuclei1/outs/filtered/matrix.mtx.gz.

It seems that the main error is "IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT"
I don't know if it is related with a sequencing problem or I should change some parameters.

Can you help me, please?

Thank you in advance!
@zhouyiqi91
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It looks like the R1 fastq file is truncated, which causes an error when automatically detecting chemistry. Chemistry can be specified explicitly to skip automatic detection of chemistry:

multi_rna \
 --chemistry scopeV3.0.1 \
..

@calcaidecabello
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calcaidecabello commented May 15, 2024 via email

@calcaidecabello
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calcaidecabello commented May 15, 2024 via email

@zhouyiqi91
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zhouyiqi91 commented May 15, 2024 •
edited

Would you please check the length read of R1 fastq reads? Are their lengths 61bp like the read in the error report?
scopeV3.0.1 requires a minimum R1 read length of 72bp

It seems that the main error is "IndexError: sequence length is not enough in R1 read: TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT"

@calcaidecabello
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calcaidecabello commented May 15, 2024 via email

@zhouyiqi91
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It seems that at least one R1 read is 61bp in length, which does not meet the minimum requirement of 72bp.
You can use grep to find this read.
zcat {R1 fastq.gz} | grep -B 1 -A 2 TGCCTGATCCGAACATGTAGGTCTCTGTCGGTGTGACTACGTATTAGCATGTGTCTGAACT

In theory, the length of each read of the raw data should be the same. Why does this short read appear? Maybe

  • The fastq file is truncated.
  • The sequencing software has done some special processing.

While it may be important to find the reason for the short read length, here are some ways to bypass this error:

  • Use the new nextflow-based pipeline: https://github.com/singleron-RD/scrna ; no R1 read minimum length check is performed.
  • Use the v2.0.7_no_R1_len_check branch where R1 read minimum length check is disabled.
git clone -b v2.0.7_no_R1_len_check --single-branch https://github.com/singleron-RD/CeleScope.git
conda activate celescope
pip uninstall celescope
cd CeleScope
pip install .

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tuqiang2014 commented May 24, 2024 •
edited

您好，请问当测序R1 pattern 是这样的 C9L16C9L16C9U12=71bp，该如何正确运行celescope呢？

回复： 参考#276 这里。设置 以下参数 ：--chemistry customized --pattern --whitelist

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@tuqiang2014 @zhouyiqi91 @calcaidecabello