Question: empty SAM file
0
gravatar for indrani.sarkar89
9 weeks 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 • 172 views
ADD COMMENTlink written 9 weeks 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 9 weeks ago by WouterDeCoster21k

For ChIP-seq bowtie1 is appropriate.

ADD REPLYlink written 9 weeks ago by genomax33k

Alright good to know.

ADD REPLYlink written 9 weeks ago by WouterDeCoster21k

Hi,

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

ADD REPLYlink written 9 weeks ago by indrani.sarkar890
1
gravatar for Rohit
9 weeks ago by
Rohit1.2k
European union
Rohit1.2k 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 9 weeks ago • written 9 weeks ago by Rohit1.2k
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