User: lolec

gravatar for lolec
lolec10
Reputation:
10
Status:
New User
Location:
France
Last seen:
1 month ago
Joined:
3 years, 2 months ago
Email:
l**************@gmail.com

Posts by lolec

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Minimap2: supplementary alignment PAF
... Hi, According to [minimap2][1] man page, the "tp" tag in the thirteenth column indicates the type of alignment: either primary, secondary or inversion. Therefore, if you want only primary or supplementary, you can simply filter as follow : awk '($13~"tp:A:P") {print $0}' file.paf > filte ...
written 10 months ago by lolec10
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Comment: C: Inconsistency between htseq-count output sorted by position or by name
... Unfortunately no. It might be inherent to how HTSEQ-count works. ...
written 2.7 years ago by lolec10
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Comment: C: What does this Warning in HTSeq-count means? (Warning: Mate pairing was ambiguou
... Hi! Did you manage to figure out why some reads have the same name? I think I have the same issue with my data. ...
written 3.1 years ago by lolec10
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Comment: C: Inconsistency between htseq-count output sorted by position or by name
... Okay, I will do that. Thank you for your help. ...
written 3.2 years ago by lolec10
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Comment: C: Inconsistency between htseq-count output sorted by position or by name
... There is no 'warning' when sorted by name. Then I don't thing the problem is coming from reads' name. The bam was obtained with TOPHAT2. ...
written 3.2 years ago by lolec10
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Inconsistency between htseq-count output sorted by position or by name
... Hello everyone! I am using htseq-count (version 0.6.1p1) on paired-end RNA seq data. I did the analysis sorting by name and sorting by position, however I obtained different results. By name: samtools sort -n accepted_hits.bam -o accepted_nsorted.bam python -m HTSeq.scripts.count -f bam - ...
htseq-count rna-seq written 3.2 years ago by lolec10

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Popular Question 17 months ago, created a question with more than 1,000 views. For Inconsistency between htseq-count output sorted by position or by name

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