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bowtie2 -q -U unmapped.fastq -x /Drive1/find_circ/index/bow2_homo --reorder --mm --very-sensitive --score-min=C,-15,0 | /home/aclab/apps/find_circ/find_circ.py -G /home/aclab/homo.fa -p homo --stats homo_sites.log --reads homo.fa >homo.bed
[E::sam_parse1] query name too long
[W::sam_read1] Parse error at line 643
Traceback (most recent call last):
File "/home/aclab/apps/find_circ/find_circ.py", line 705, in
sam_line = pair_num * 2
NameError: name 'pair_num' is not defined
""I used single read fastq file and it varies in length and the unmapped fastq file look like::
bf0c7879-f557-4fd4-bbfa-2e789855dc27_A__TTTGACCAAGAAGAGATACGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTGGACTTGATTGTTGACGCCATCAAGGCTGCTGGTCACGACGGTAAGGTCAAGATCGGTTTGGACTGTGCTCTGAATTCTTCAAGGACGGTAAGTACGACTTGGACTTAGAACCCAGAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTAGACATGTACCGCCTTGATGAAGAGATACCCAATTGTCTCCATCGAAGATCCATTTGCTGAAAGATGACTGGGAAGCTTGGGTCTCACTTCAAGACCGCTGGTATCCAAATTGTTGCTGATGACTTGACTGTCACCAACCCAGCTAGAATTATACCGCCATCGAAAGAAGGCTGCTGACGCTTTGGTTAGCGTTGAAGGTTAACCAAATCGGTACCTTGTCTGAATCCATCAAGGCTGCTCAAGACTTCGCAGCCAACTGGGTGTCATGGTTTCCCACAGATCTGGCTGAAACTGAAGACACTTTCTCATTGCTGACTTGGTTGTCGGTTTGAAGAACTGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAGATTGGCTAAGTTGAACCAATTGTTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTATGCCGGTAG
TTTGACCAAGAAGAGATACG
+
($(<78<?FBFK=$'0
@bf0c7879-f557-4fd4-bbfa-2e789855dc27_B
AAGGCTGTCTATGCCGGTAG
+
??86*+6,(*((0217:'$.
837dd288-73fd-40ab-9acb-4e3a455c0562_A__AATTCATGATTGCCTTAACTGGTGCTAAGACCTCTGAAGCCAAAGAATTGGTTCCGGTTTACCACAACTTGAAGTCTTTGACCAAGAAGAGATTCGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGCTGGTCACACGGTAAGGTCAAGATCGGTTTGGACTGTGCCACCTTGAATTCAAGGACGGTAAGTACGACTTGGACTCAAGAACCCAGAAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTGACATGTACCATTTCCTTGATGAAGAGATACTCAATTGTCTCCATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCTTGGTCTCATTTTCAAGACCGTTGGTATCCAAATATCGTTGATGACTTGACTGTCACCATTCCCGGCTAGAATTCGCCAAAGAAGGCTGCTGACGCTTTGTTGTTGAAGTTAACCAATTCAAGTACCTTGTCTGAAACCCATCAAGGCTGCTCAAGACTCATTGCCAACTTGGGGTGTCATGGTTTCCCACAGATCTGGTGAAAACTGAAGACTTCATTGCTGACTTGGTTGTCGGTTTGAGAACGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAAGATTGGCTAAGTTGAACCAATTGTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTACGCCGGTG
AATTCATGATTGCCTTAACT
So plz can you tell me is it possible to run find_circ on this fastq file. If yes then please suggest me.
Thanks in advance
The text was updated successfully, but these errors were encountered:
@aman21392: I'd suggest you have a look at https://github.com/rajewsky-lab/find_circ2 and if you have issues with this version, open a new issue there. Also, make sure to include what operating system you are on and how you installed the software if you want people to be able to help you.
bowtie2 -q -U unmapped.fastq -x /Drive1/find_circ/index/bow2_homo --reorder --mm --very-sensitive --score-min=C,-15,0 | /home/aclab/apps/find_circ/find_circ.py -G /home/aclab/homo.fa -p homo --stats homo_sites.log --reads homo.fa >homo.bed
[E::sam_parse1] query name too long
[W::sam_read1] Parse error at line 643
Traceback (most recent call last):
File "/home/aclab/apps/find_circ/find_circ.py", line 705, in
sam_line = pair_num * 2
NameError: name 'pair_num' is not defined
""I used single read fastq file and it varies in length and the unmapped fastq file look like::$(<78<?FBFK=$ '0
bf0c7879-f557-4fd4-bbfa-2e789855dc27_A__TTTGACCAAGAAGAGATACGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTGGACTTGATTGTTGACGCCATCAAGGCTGCTGGTCACGACGGTAAGGTCAAGATCGGTTTGGACTGTGCTCTGAATTCTTCAAGGACGGTAAGTACGACTTGGACTTAGAACCCAGAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTAGACATGTACCGCCTTGATGAAGAGATACCCAATTGTCTCCATCGAAGATCCATTTGCTGAAAGATGACTGGGAAGCTTGGGTCTCACTTCAAGACCGCTGGTATCCAAATTGTTGCTGATGACTTGACTGTCACCAACCCAGCTAGAATTATACCGCCATCGAAAGAAGGCTGCTGACGCTTTGGTTAGCGTTGAAGGTTAACCAAATCGGTACCTTGTCTGAATCCATCAAGGCTGCTCAAGACTTCGCAGCCAACTGGGTGTCATGGTTTCCCACAGATCTGGCTGAAACTGAAGACACTTTCTCATTGCTGACTTGGTTGTCGGTTTGAAGAACTGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAGATTGGCTAAGTTGAACCAATTGTTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTATGCCGGTAG
TTTGACCAAGAAGAGATACG
+
(
@bf0c7879-f557-4fd4-bbfa-2e789855dc27_B
AAGGCTGTCTATGCCGGTAG
+
??86*+6,(*((0217:'$.
837dd288-73fd-40ab-9acb-4e3a455c0562_A__AATTCATGATTGCCTTAACTGGTGCTAAGACCTCTGAAGCCAAAGAATTGGTTCCGGTTTACCACAACTTGAAGTCTTTGACCAAGAAGAGATTCGGTGCTTCTGCCGGTAACGTCGGTGACGAAGGTGGTGTTGCTCCAAACATTCAAACCGCTGAAGAAGCTTTGGACTTGATTGTTGACGCTATCAAGGCTGCTGGTCACACGGTAAGGTCAAGATCGGTTTGGACTGTGCCACCTTGAATTCAAGGACGGTAAGTACGACTTGGACTCAAGAACCCAGAAATCTGACAAATCCAAGTGGTTGACTGGTGTCGAATTGGCTGACATGTACCATTTCCTTGATGAAGAGATACTCAATTGTCTCCATCGAAGATCCATTTGCTGAAGATGACTGGGAAGCTTGGTCTCATTTTCAAGACCGTTGGTATCCAAATATCGTTGATGACTTGACTGTCACCATTCCCGGCTAGAATTCGCCAAAGAAGGCTGCTGACGCTTTGTTGTTGAAGTTAACCAATTCAAGTACCTTGTCTGAAACCCATCAAGGCTGCTCAAGACTCATTGCCAACTTGGGGTGTCATGGTTTCCCACAGATCTGGTGAAAACTGAAGACTTCATTGCTGACTTGGTTGTCGGTTTGAGAACGGTCAAATCAAGACTGGTGCTCCAGCTAGATCCGAAAAGATTGGCTAAGTTGAACCAATTGTGAGAATCGAAGAAGAATTGGGTGACAAGGCTGTCTACGCCGGTG
AATTCATGATTGCCTTAACT
So plz can you tell me is it possible to run find_circ on this fastq file. If yes then please suggest me.
Thanks in advance
The text was updated successfully, but these errors were encountered: