--u option in bowtie2

Question

[zizigolu]

Hi

In the rRNA filtering part I am going to map the fastq reads on the rRNA sequences and keep only the reads which has not been mapped, in cmd I should type:

bowtie2 -x [name of the bowtie2-build indicized file containing the rRNA sequence] \
  --un [name of the fastq file which will contain the UNMAPPED reads] \
  -U [name of the fastq file containing the reads] \
  -S [name of the .sam file that will contain the MAPPED and UNMAPPED reads]

I could not understand about --un option because I don't know which I should type instead of [name of the fastq file which will contain the UNMAPPED reads].

Is the name optional? I typed some optional names with gz Suffix but always error

[jivarajivaraj]

I typed --un unmapped.fastq

But it saying that:

warning bowtie2-align run directly. it is recommended that you run the wrapper script "bowtie2" instead

I am going to have two files: one sam file containing mapped and unmapped reads and another file containing unmapped reads by --un option but I don't know for afresh file which name I should type or totally why I get error...`

Please help me more if possible

[Ram]

Please move this to a separate question. And paste your full command when you create the new question.

[Devon Ryan]

In addition to what Ram said, read the error message. It's telling you what you did wrong.

[zizigolu]

Devon,

As I typed the error for Ram, when I used bowtie2 instead of bowtie2_align, it says not recognized as external or internal command

[Devon Ryan]

Ensure that bowtie2 is in the same directory. You'll need to have perl installed. I actually have no idea if any of this will work on Windows, there's a reason people don't use it in Bioinformatics.

[Ram]

How did you know OP was using Windows? And why does it look like "sarah" and "jivarajjivaraj" are the same person/working together?

[zizigolu]

hey Ram, please

I need help not being searched by bioinformatics detectives!!

You suppose she knows me well but cant help more just sharing my question

[Ram]

You are mistaken if you think that someone sharing your question on a separate thread helps your case. Mods will redirect the person to your question and close the new question. That is standard policy in any forum. Plus, this other user does not have the requisite reputation to add a positive effect (in fact, their usage patterns are frankly quite odd)

And if a second user posts a related question on your thread, people's attention will be diverted between the subject matters, and this is called "hijacking the thread". We do this only to ensure usage etiquette is followed so you can get quick answers.

[zizigolu]

:(

Thanks Devon

Answer 1

[Ram]

You should type in the name for a file which will be created afresh to hold unmapped reads. Ensure the name you provide ends with a .fastq