HTSeq command option for single-end reads
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@4fedfa78
Last seen 24 months ago
Japan

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Code should be placed in three backticks as shown below Hello,

I have a question regarding HTSeq count software option which I am confuse what it should be when my read is single-end. This is the option:

-s <yes/no/reverse>, --stranded=<yes/no/reverse>

#I used the HTSeq command for single end as below:

htseq-count -s yes SRR0000.sam  hg19.ensGene.gtf > SRR00000

but I am not sure whether I use yes/no/reverse for single-end reads? 


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# please also include the results of running the following in an R session 

sessionInfo( )
HTSeqGenie • 1.9k views
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Depends on whether your library is stranded or not. Ask the person who produced it.

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Many thanks for your reply. can I know if it is stranded which option should be used and which for non-stranded in single end reads?

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If forward-stranded (rare) it is yes, if reverse-stranded (common) then reverse, else no.

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Thanks a lot for your help. Could you please answer these questions, I would really appreciate it.

Just I am still a bit confuse in case if I do not know it is forward or reverse stranded, so it means I must use "no"?

and could you please tell me what option should I use if it is paired ends?

and what option should I use if it is non-stranded?

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Ok, again as clear as I possibly can:

If your library is forward-stranded, then use yes.

If your library is reverse-stranded, then use reverse.

If your library is unstranded, or you are ok with pretending it was unstranded, or you don't care, then use no.

Everything else, so paired-end support and how to use HTseq is explained in the docs, please read it: https://htseq.readthedocs.io/en/release_0.11.1/count.html

Ask the person who made the library or use something like http://rseqc.sourceforge.net/#infer-experiment-py to make a guess based on the data. Good luck.

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Thanks in advance for your help and cooperation. I do really appreciate it.

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