--u option in bowtie2
Hi
I am going to have two files: one sam file containing mapped and unmapped reads and another file containing just unmapped reads by --un option by this command (windows)
bowtie2-align-s.exe -x arabidopsis_genome `--un unmapped.fastq` -U C:\seq\GSM575243.fasta -S eg1.sam
but I don't know for afresh file which name I should type or totally why I am facing this error:
warning bowtie2-align run directly. it is recommended that you run the wrapper script "bowtie2" instead
then how I can have two separate files with --un option?
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Run bowtie2 instead of
bowtie2-align-s.exe -xPS: I just saw that you have already asked this question. Please wait for people to respond to your other post before opening a new post. Thanks.
Ram asked me to open a new question!
I asked jivarajivaraj to open a new question, sarah, not you. This is what made me wonder if you two are the same person with multiple accounts. And if that is the case, you see how this can lead to confusion.
Hello sarah!
This is a duplicate post (see: --u option in bowtie2). There appears to have been some confusing about comments to another user. No need to provide answers here too.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!