tagAlign to BAM

Question

[rbronste]

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?

Answer 1

[venu]

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.

[rbronste]

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?

[venu]

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).