Question: tagAlign to BAM
0
gravatar for rbronste
22 months ago by
rbronste260
rbronste260 wrote:

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?

tagalign bam encode • 1.0k views
ADD COMMENTlink modified 22 months ago by venu6.2k • written 22 months ago by rbronste260
1
gravatar for venu
22 months ago by
venu6.2k
Germany
venu6.2k wrote:

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.

ADD COMMENTlink written 22 months ago by venu6.2k

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?

ADD REPLYlink written 22 months ago by rbronste260

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).

ADD REPLYlink written 22 months ago by venu6.2k
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