Question: Is It Okay To Remove Chrun And Chr*_Random Reads From A Bed File?
3
gravatar for danielcook2013
5.8 years ago by
danielcook201370 wrote:

Do these reads hold any value? Are there software tools that make use of them? Just curious - because I was having trouble using liftover when they are present...

chip-seq • 2.3k views
ADD COMMENTlink modified 5.8 years ago by Jorge Amigo11k • written 5.8 years ago by danielcook201370
4

I normally remove them after I am done with the alignment of reads. But I keep them for alignment.

ADD REPLYlink written 5.8 years ago by Ashutosh Pandey11k
1

I would also support keeping them for alignment. The reason for me is that if I don't, I might get extra reads mapping to the main chromosomes when they would otherwise have mapped to the rermoved sequences. However, for certain operations like peak calling in DNA-seq, I remove them as I think they can mess up certain normalization procedures.

ADD REPLYlink written 5.8 years ago by KCC3.9k

Keeping reads that map to chrM, chrUn, etc certainly have a detrimental effect on MACS (ChIP-seq peak caller) statistics.

ADD REPLYlink written 5.8 years ago by Ian5.5k
2
gravatar for Mikael Huss
5.8 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

I don't see any danger in removing them for liftOver (indeed it may be necessary to do it). They might be of interest in some rare cases such as evaluation of mapping software, characterizing multimapping reads etc - but as for myself, I have never really used them.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Mikael Huss4.6k
1
gravatar for Jorge Amigo
5.8 years ago by
Jorge Amigo11k
Santiago de Compostela, Spain
Jorge Amigo11k wrote:

it really depends on what your bed file is used for. for instance, we use them to define regions of interest, which are used for defining the sequencing experiment and also through the downstream analysis to focus in particular regions of our bam alignments and perform operations on such particular loci. although we may end up after alignment with reads that would have aligned to chrUn* or chr*_random, since the knowledge we aim to obtain is not to be contained on such contigs, we do not consider them when ultimately reporting variants or coverage. we still leave those reads on the bam file in case a new aligner is able to position them somewhere else, or if any particular experiment would be interested in looking to that contigs in particular, but since this is not the daily usage that's the main reason why we never include them in our experiment designs' bed files.

ADD COMMENTlink written 5.8 years ago by Jorge Amigo11k
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