Question: empty SAM file
0
gravatar for indrani.sarkar89
11 months ago by
indrani.sarkar890 wrote:

Hi,

I am very new to chip-seq analysis. I have used bowtie -m 1 -S bowtie_index/mm10 Oct4.fastq > Oct4.sam to generate the sam file. However, after the run in complete, the generated sam file is empty. Please suggest what should I do? I was trying the sample provided by EMBL-EBI training when I got the problem...

chip-seq • 438 views
ADD COMMENTlink written 11 months ago by indrani.sarkar890

This is probably not related to this issue and I'm not entirely sure, but shouldn't you be using bowtie2?

ADD REPLYlink written 11 months ago by WouterDeCoster29k

For ChIP-seq bowtie1 is appropriate.

ADD REPLYlink written 11 months ago by genomax49k

Alright good to know.

ADD REPLYlink written 11 months ago by WouterDeCoster29k

Hi,

It worked...it was actually a typing error...

ADD REPLYlink written 11 months ago by indrani.sarkar890
1
gravatar for Rohit
11 months ago by
Rohit1.3k
European union
Rohit1.3k wrote:

Isn't the command bowtie -m 1 -S bowtie_index/mm10 Oct4.fastq Oct4.sam

You don't need a directed output ">"

ADD COMMENTlink modified 11 months ago • written 11 months ago by Rohit1.3k
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