Question: Soft-clipping primers from BAM introduces errors. Solution?
0
gravatar for lamteva.vera
2.1 years ago by
lamteva.vera160
Ukraine, Kyiv
lamteva.vera160 wrote:

Dear all,

I work with paired-end amplicon data. Following the recommendations of the bioinformatics community, I soft-clip primer sequences from BAM files (see my post if you are looking for tools designed to perform this task).

So far, I've tried soft-clipping primer sequences with BamClipper and Katana. Each of the tools has introduced errors into the BAM files. Here are the exemplary outputs of ValidateSamFile (MODE=SUMMARY, IGNORE_WARNINGS=false):

  1. After BamClipper:

HISTOGRAM java.lang.String Error Type Count

ERROR:INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT 60

ERROR:INVALID_MAPPING_QUALITY 129

ERROR:MISMATCH_FLAG_MATE_UNMAPPED 78

ERROR:MISMATCH_MATE_ALIGNMENT_START 4934

ERROR:MISMATCH_MATE_CIGAR_STRING 1427718

WARNING:MISSING_TAG_NM 1428978

  1. After Katana:

HISTOGRAM java.lang.String Error Type Count

ERROR:INVALID_UNALIGNED_MATE_START 54543

ERROR:MISMATCH_MATE_CIGAR_STRING 2146704

Is it expected to get such errors after soft-clipping sequences? Why did they occur? And, more practically, how to fix them?

ADD COMMENTlink written 2.1 years ago by lamteva.vera160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1001 users visited in the last hour