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Hi,
I'm working with GTEx RNA-Seq BAM files. Their general trouble is that somehow many of them if not all have different headers. The differences are only in the number of those elements like GL000195.1 etc.
Different headers lead to inability of several programs to work with the batch of such BAMs.
I focus only in a couple of genes on one chromosome. So I decided to filter only the reads mapped to the genomic region of interest. Then I changed the headers of the new filtered BAMs via 'samtools reheader' removing all that GL000... lines. As a result, all the new BAMs have the same header in terms of @SQ lines. And here is a problem. I can't index these BAMs. Samtools simply produces one line of output: Segmentation fault.
I have two questions:
1) Could you advise me how to get indexed BAMs with the uniform (@SQ lines) headers.
2) I don't understand why samtools couldn't index reheaded BAMs? Even if I keep in such BAMs only those reads that were mapped only to chr5 to the specific gene. What might cause a problem if in the alignment info for every read in these reheaded BAMs there are no information at all about any GL... elements (or, actually, any other chromosomes). What is so critical in the header @SQ lines for other elements that are not represented among the reads in the BAMs?
Thanks!
I'm working with GTEx RNA-Seq BAM files. Their general trouble is that somehow many of them if not all have different headers. The differences are only in the number of those elements like GL000195.1 etc.
Different headers lead to inability of several programs to work with the batch of such BAMs.
I focus only in a couple of genes on one chromosome. So I decided to filter only the reads mapped to the genomic region of interest. Then I changed the headers of the new filtered BAMs via 'samtools reheader' removing all that GL000... lines. As a result, all the new BAMs have the same header in terms of @SQ lines. And here is a problem. I can't index these BAMs. Samtools simply produces one line of output: Segmentation fault.
I have two questions:
1) Could you advise me how to get indexed BAMs with the uniform (@SQ lines) headers.
2) I don't understand why samtools couldn't index reheaded BAMs? Even if I keep in such BAMs only those reads that were mapped only to chr5 to the specific gene. What might cause a problem if in the alignment info for every read in these reheaded BAMs there are no information at all about any GL... elements (or, actually, any other chromosomes). What is so critical in the header @SQ lines for other elements that are not represented among the reads in the BAMs?
Thanks!
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