Hi,
I am trying to use bwa and samtools to see if in the CEU transcriptome there are multiple splice variants of a couple of genes.
I got the CEU transcriptome from here:
(I used the fastq files), and I went on to use bwa to
1) align the fastq reads to my reference file with the possible splices
2) creating a sam file from (1)
Now I have transformed the sam files in bam files, and additionally sorted and indexed them.
What I want to do now is the following: see a (m)pileup of my reference splices against the bam files (161 bam files in total).
My problem is that I am running everything on a cluster, so I cannot run samtools mpileup to give me an interactive view of the alignment.
What I'd like to do is to get out of samtools some output text file that tells me, for every bam file, if there is anything aligning to my splices, and some sort of read depth/other quality score/p-value/whatever.
Any idea on how to do that? I am running out of ideas (I self taught bwa and samtools in the last 3 days, so I feel I am running out of my intuition).
I am trying to use bwa and samtools to see if in the CEU transcriptome there are multiple splice variants of a couple of genes.
I got the CEU transcriptome from here:
(I used the fastq files), and I went on to use bwa to
1) align the fastq reads to my reference file with the possible splices
2) creating a sam file from (1)
Now I have transformed the sam files in bam files, and additionally sorted and indexed them.
What I want to do now is the following: see a (m)pileup of my reference splices against the bam files (161 bam files in total).
My problem is that I am running everything on a cluster, so I cannot run samtools mpileup to give me an interactive view of the alignment.
What I'd like to do is to get out of samtools some output text file that tells me, for every bam file, if there is anything aligning to my splices, and some sort of read depth/other quality score/p-value/whatever.
Any idea on how to do that? I am running out of ideas (I self taught bwa and samtools in the last 3 days, so I feel I am running out of my intuition).
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