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tagAlign to BAM

Wondering if anyone knows how to convert the ENCODE generated tagAlign file (combo of several replicate BAMs) into a merged BAM file? Or is it necessary to take the individual replicate bam's and merge them separately?

encode tagalign bam
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updated by venu venu • written by rbronste rbronste

1 answer

bedToBam function from bedtools suite.

Ex: including sorting the bam

bedToBam -i <(zcat E129-H3K27ac.tagAlign.gz) -g hg19.sizes | samtools sort - E129-H3K27ac

And samtools merge option for merging replicates / merging peaks from different replicates is also an option.

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written by venu venu

Thanks!

So it processed it but with the following error: 

[bam_header_read] EOF marker is absent. The input is probably truncated.

Wondering if it is critical to have that EOF marker?

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written by rbronste rbronste

Where exactly this happened ? (A long back I read in this forum (can't find it now) that if the output file is generated as usual, we don't need to bother about this warning).

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written by venu venu

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