Hi All,
SortMeRNA is useful to remove rRNAs. Do you know any option to save these rRNA reads? I want to do some further analysis to these rRNAs.
Thanks.
The website says
SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments.
(emphasis added by me)
What is the problem you're facing, exactly?
my problem is I want to the know which option could let me receive all the rRNA reads.
the usage document of sortmerna is too bad.
No. that's why I said the usage is bad.
It's not. 30 seconds of effort gives me this link from the webpage I pointed to above: https://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v2.1.pdf
The manual has this text:
[COMMON OPTIONS]: --other STRING rejected reads filepath + base file name (appropriate extension will be added)
and this text:
[HELP]: -h BOOL help
So please tell me how my statement ("you would rather we do it for you") is incorrect.
What's your point? the -- other file is rRNA reads?
My point is that there are only two prefixes - the -other and the -aligned. The tool documentation says that it writes rRNA reads out, so it has to be one of them that it writes to. It's your job to figure out beyond this point. If you were unsure which output file the rRNA reads are in, that should have been your question, not "is there an option to save the rRNA reads".
The former shows you've tried investing effort and are confused about a specific point, whereas the latter shows that you can just ask us to do your job for you.
And to address your deleted comment ("do you read my question? and do you think your answer is to solve my question? do you know what -other option give you?"), yes I did read your question and my answer does "solve" it.
That's why I ask this question. There is no exactly explain for this easy question in the usage documents. and that's why I come to ask for the confirmation from the experts and thanks you answered my question even that you didn't give a confirmed answer. Thanks all the same 30 second SIR
Sure, you are definitely a genius in this world.
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