empty SAM file
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...
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indrani.sarkar89 •
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This is probably not related to this issue and I'm not entirely sure, but shouldn't you be using bowtie2?
For ChIP-seq bowtie1 is appropriate.
Alright good to know.
Hi,
It worked...it was actually a typing error...