I found your pipeline very interesting, since I have the same sample analyzed with both indrop and 10x, but is impossible to compare different pipelines.
Therefore I tried to run your full pipeline but the folder read_tagging remained empty. Therefore I decided to run the alignment and the read_tagging steps separately. The alignment step I believe went fine ( in star_align I have subfolders AA, AC, etc and inside each of them there are several files, including the **.sort.bam file).
However when I try to run only the tagging step with: baseq-Drop run_pipe --step tagging --config ./config_drops.ini -g hg38 -p indrop --minreads 10000 -n testrun -1 ./R1.fastq.gz -2 ./R2.fastq.gz -d ./
...I have an error regarding a missing file "genes_transcript.txt".
I wonder where does this file comes from, by reading the script tag_reads.py I really have hard time understanding when this file is generated.
Any help and additional documentation would be really appreciated.
Thanks in advance
I found your pipeline very interesting, since I have the same sample analyzed with both indrop and 10x, but is impossible to compare different pipelines.
Therefore I tried to run your full pipeline but the folder read_tagging remained empty. Therefore I decided to run the alignment and the read_tagging steps separately. The alignment step I believe went fine ( in star_align I have subfolders AA, AC, etc and inside each of them there are several files, including the **.sort.bam file).
However when I try to run only the tagging step with: baseq-Drop run_pipe --step tagging --config ./config_drops.ini -g hg38 -p indrop --minreads 10000 -n testrun -1 ./R1.fastq.gz -2 ./R2.fastq.gz -d ./
...I have an error regarding a missing file "genes_transcript.txt".
I wonder where does this file comes from, by reading the script tag_reads.py I really have hard time understanding when this file is generated.
Any help and additional documentation would be really appreciated.
Thanks in advance