Question: (Closed) --u option in bowtie2
gravatar for Angel
4.4 years ago by
Angel3.5k wrote:


i am going to have tow 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 dont 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?

sequencing • 1.2k views
ADD COMMENTlink written 4.4 years ago by Angel3.5k

run bowtie2 instead of bowtie2-align-s.exe -x

PS: 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.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by Ashutosh Pandey11k

Ram asked me to open a new question!

ADD REPLYlink written 4.4 years ago by Angel3.5k

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.

ADD REPLYlink written 4.4 years ago by RamRS24k

Hello sarah!

This is a duplicate post (see: 141531). 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.


ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by SES8.2k
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