Pre-processing for diffHiC
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@james-w-macdonald-5106
Last seen 2 days ago
United States

After aligning data using the presplit_map.py Python script, the next recommended step is to use Picard FixMateInformation and MarkDuplicates. However, using the current version of Picard I get

Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name K00280:111:HWNMLBBXX:7:1101:1174:14643, Mapped mate should have mate reference name

Which is hogwash:

$ samtools view 1-1.bam | head -n 4 | cut -f 1-2
K00280:111:HWNMLBBXX:7:1101:1174:14643    81
K00280:111:HWNMLBBXX:7:1101:1174:14643    145
K00280:111:HWNMLBBXX:7:1101:1174:14713    2049
K00280:111:HWNMLBBXX:7:1101:1174:14713    81

Anyway, is there some trickeration that needs to be done (other than using VALIDATION_STRINGENCY=DONTBOTHERMEABOUTFAKESTUFF)?

diffHiC • 309 views
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Aaron Lun ★ 27k
@alun
Last seen 2 hours ago
The city by the bay

Looking at https://github.com/LTLA/diffHicUsersGuide/blob/master/sra2bam.sh indicates that I did indeed set VALIDATION_STRINGENCY=SILENT. I recall that Picard would complain about everything and anything (especially prior to fixing the mate information) so you end up having to set this flag all the time.

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Thanks Aaron. SILENT seems to be the hot ticket. LENIENT, not so much.

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