Question: Identifying distance between mate pairs
0
gravatar for onspotproductions
3.4 years ago by
United States
onspotproductions130 wrote:

I would like to know of a few tools for identifying distances between mate pairs on datasets where that is not given.

ADD COMMENTlink modified 3.4 years ago by h.mon24k • written 3.4 years ago by onspotproductions130
2
gravatar for Biomonika (Noolean)
3.4 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

REAPR

picard's CollectInsertSizeMetrics (https://broadinstitute.github.io/picard/command-line-overview.html)

ADD COMMENTlink written 3.4 years ago by Biomonika (Noolean)3.0k
0
gravatar for h.mon
3.4 years ago by
h.mon24k
Brazil
h.mon24k wrote:

You can get a biased estimate by merging overlapping pairs and measuring the resulting sequence sizes, or you can map to a reference genome and estimate insert size. BBMerge can merge reads and output an insert size histogram, BBMap can map and also output an insert size histogram.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by h.mon24k
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