User: Glubbdrubb

gravatar for Glubbdrubb
Glubbdrubb0
Reputation:
0
Status:
New User
Last seen:
2 months ago
Joined:
2 months, 1 week ago
Email:
v***********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by Glubbdrubb

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... That didn't reveal anything. I think the invisible character is lost when I extract the lines. But then I did a diff of the original and cleaned files: diff -c sample.sam D8_Bird8_42-3p.sam | less This reveals the rather odd <82> near the end of the affected lines. Sometimes it even repe ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... Yes, but keep in mind those are octal ascii codes, not decimal ascii codes. Removing only 160 (which is 240 octal) did not make any difference to the file. ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... What is the octal encoding for ASCII 160 in octal? Cause my tr command requires octal specifications. I assumed 160 is decimal, and according to http://ascii-table.com/calculator.php , 160 dec encodes to 240 octal. I deleted all of those characters using tr -d '\240' < D8_Bird8_42-3p.sam &g ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... The bam files were only worked on in Linux, using linux tools. I wrote a python script that printed the line number of the first line that produces an error. https://pastebin.com/TEki6jhe This produces exactly the same error as htseq-count if I don't catch the exception. When I examined the offe ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... Ah yes, my mistake. I misread the description of sam fields. Yup, those bam files worked in htseq-count and htseq-qa (qa can only accept sam files, so I converted them first). Here's an example line from a bam file that worked: FCC4MT3ACXX:8:1109:8871:93069# 419 PRELSG_01_v1 1 1 ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... I meant lower case, not lower value.. I have 18 bam files, 10 of them work without a problem. Just some info about the nature of the source data: The paired-end reads in the FASTQ files are trimmed. ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... It is a Plasmodium relictum genome from PlasmoDB. And I can't explain these oddities in the bam file. Especially since most of the samples work fine in htseq-count. When I view the bam file in less (piped in from samtools view), all the white spaces are tabs, but not all tabs are the same length. Yo ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... I did that. The resulting bam file is about a third smaller. But htseq count produced the same "ordinal not in range" error. Here is the corresponding record in the new bam file: FCC4MT3ACXX:7:2203:9969:30526# 163 PRELSG_06_v1 268502 255 75M = 268607 258 CCTACATCACCA ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... I get an empty result with that. I don't think STAR produces bam files with unmapped reads using the default parameters. ...
written 9 weeks ago by Glubbdrubb0
0
votes
1
answer
277
views
1
answers
Comment: C: htseq-count SAM Processing error "can't decode byte 0xa7"
... htseq version 0.11.0 htseq-count -q -t exon -f bam -r pos -s no -m union mapped_reads/D8_Bird8_42-3p.bam p.relictum/PlasmoDB_genome/PlasmoDB-39_PrelictumSGS1-like.gtf > htseq_count/D8_Bird8_42-3p.count ...
written 9 weeks ago by Glubbdrubb0

Latest awards to Glubbdrubb

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 755 users visited in the last hour