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questions
1
vote
2
replies
687
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Error correction based on PCR duplicates using clumpify.sh
RNAseq
bbmap
duplicates
clumpify
2.3 years ago by
lechu
▴ 20
0
votes
1
reply
547
views
Clipping bases from non-overlapping regions of mate reads in BAM file
RNAseq
updated 2.4 years ago by
Pierre Lindenbaum
161k • written 2.4 years ago by
lechu
▴ 20
1
vote
5
replies
2.4k
views
Soft-clipping of a BAM file based on regions from the BED file
rna-seq
updated 3.1 years ago by
Pierre Lindenbaum
161k • written 3.1 years ago by
lechu
▴ 20
0
votes
0
replies
727
views
Adding information tags with types, positions and counts of matches and mismatches in every read in the SAM file
RNA-Seq
3.2 years ago by
lechu
▴ 20
0
votes
0
replies
430
views
How to get coverage for specific base(s), and for specific mismatch(es) per genomic range
RNA-Seq
3.2 years ago by
lechu
▴ 20
2
votes
5
replies
992
views
Annotating reads with the name of the feature to which they map
RNA-Seq
updated 3.2 years ago by
A. Domingues
★ 2.7k • written 3.2 years ago by
lechu
▴ 20
0
votes
0
replies
575
views
Mapping long RNAseq reads to genome with nextGenMap - how to adjust parameters?
RNA-Seq
3.2 years ago by
lechu
▴ 20
0
votes
6
replies
1.3k
views
How to modify a BAM file to avoid double-counting of variants from overlapping PE reads?
RNA-Seq
BSseq
3.2 years ago by
lechu
▴ 20
0
votes
2
replies
1.0k
views
Merging overlapping mates in a BAM / SAM file into one read
RNA-Seq
3.2 years ago by
lechu
▴ 20
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