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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?
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
sessionInfo( )
Depends on whether your library is stranded or not. Ask the person who produced it.
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?
If forward-stranded (rare) it is yes, if reverse-stranded (common) then reverse, else no.
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?
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.
Thanks in advance for your help and cooperation. I do really appreciate it.