User: bnayer26

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bnayer260
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Posts by bnayer26

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Comment: C: Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... h.mon, I forgot to reply to your msg above but thanks a lot for sending those links - it really helped. I could not still get the HTseq to work seamlessly but it gives me some solace to know that the developer of the program himself recognises this as a problem. I will try other methods now. ...
written 4 months ago by bnayer260
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Comment: C: Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... Also, what does the @PG line indicate? I do not understand everything in that code per se, so if you please point out what exactly you were referring to, that would help. thank you :) Also, how do you suggest I proceed with my alignment files in that case? Does any other counting software like feat ...
written 4 months ago by bnayer260
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Comment: C: Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... Thanks h.mon, yes I had read your comment on my previous question and I had responded to you as well. Sorry I deleted it eventually because I had mixed two questions in that one, and once I wrote this question down more clearly, the previous one was redundant. I understand when you talk about HTseq ...
written 4 months ago by bnayer260
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Comment: C: Error at the end of HT-seq Analysis and output.txt with 0 bytes in size
... Hi Devon Ryan, I am facing a similar problem although there are some differences. If you don't mind could you please check the question I have recently posted here and provide some insight? Thank you (https://www.biostars.org/p/366585/) ...
written 4 months ago by bnayer260
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Comment: C: Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... I have done the needful. I have also updated the bottom part of my question. If you could help me figure this out, I'd be really grateful. Thanks. ...
written 4 months ago by bnayer260
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Comment: C: Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... Oh sorry, I had run two samples together and this was what came in the error log file for both. I will delete the lower part so that it reflects what happened with one sample only. Thanks for pointing that out. ...
written 4 months ago by bnayer260
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Error upon running HTseq with paired end aligned BAM (coordinate sorted) files
... I am using HTseq to perform counts and I'm encountering the following error, and my output .txt file is empty. 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines process ...
htseq rnaseq written 4 months ago by bnayer260 • updated 4 months ago by h.mon26k
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Comment: C: Counting number of genes using htseq-count tool.
... Hi Leipinji, I came across this post while trying to figure out the problem for myself. Could you please explain why do we need to provide a bam file which is sorted by name in HTseq? Can we provide a coordinate-sorted file and then introduce the argument "-r name" in the HTseq command instead? Is t ...
written 4 months ago by bnayer260
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Comment: C: HTseq error with paired end alignments
... I don't know at what step this "mixing" of single end reads would have happened? Could you elaborate. My raw data consisted of paired end reads only. I used that for adapter trimming with Trimmomatic, which gave me a "paired_trimmed" and an "unpaired trimmed" file for each read. Then I used both pai ...
written 4 months ago by bnayer260
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Comment: C: HTseq code error repeatedly
... Thank you for asking me that question. Due to my lack of coding knowledge it didn't even strike me that head is a command. I looked it up and found that "head" only returns the first 10 lines. Also, I learnt about "tail, less and more" commands. And upon running the less and more commands I found al ...
written 4 months ago by bnayer260

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