Hi!
I am trying to replicate some biocomputational procedures from a scientific paper related to ChIP-Seq data. When using bowtie as the alligner and introducing the output (specified as .sam format) in the MACS software it tells me that the file format is not recognized.
However, after converting the unrecognized sam file to bam format using samtools, MACS does recognize the file format and starts analyzing the data.
Could anyone shed some light on this?
My bowtie and macs commands are:
bowtie -m 2 -q -p 24 --sam hg19 File1.fastq File1.sam
macs14 callpeak -t File1.sam -c ControlFile.sam
-n ExperimentName -S -g hs --pvalue 1e-9 --keep-dup=auto
Iñigo
I am trying to replicate some biocomputational procedures from a scientific paper related to ChIP-Seq data. When using bowtie as the alligner and introducing the output (specified as .sam format) in the MACS software it tells me that the file format is not recognized.
However, after converting the unrecognized sam file to bam format using samtools, MACS does recognize the file format and starts analyzing the data.
Could anyone shed some light on this?
My bowtie and macs commands are:
bowtie -m 2 -q -p 24 --sam hg19 File1.fastq File1.sam
macs14 callpeak -t File1.sam -c ControlFile.sam
-n ExperimentName -S -g hs --pvalue 1e-9 --keep-dup=auto
Iñigo
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