featureCounts: No effect of setting -d and -D?
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@darioberaldi-6991
Last seen 10 weeks ago
United Kingdom

Using featureCounts v2.0.1, I don't see any effect in changing -d and -D options (minimum and maximum fragment/template length, respectively). My bam file has paired reads and I set the -p option. Am I missing something?

Here's example output using silly values of -d 10 -D 10000 and -d 10000 -D 10. No difference:

featureCounts -d 10 -D 10000 -a genrich/ATACseq/single/atac_merge.gff -o tmp.tsv -t peak -g locus_id -p bwa/Ap2oGFP1o.pb.bam

cat tmp.tsv.summary 
Status  bwa/Ap2oGFP1o.pb.bam
Assigned    3747979
Unassigned_Unmapped 0
Unassigned_Read_Type    0
Unassigned_Singleton    0
Unassigned_MappingQuality   0
Unassigned_Chimera  0
Unassigned_FragmentLength   0
Unassigned_Duplicate    0
Unassigned_MultiMapping 0
Unassigned_Secondary    0
Unassigned_NonSplit 0
Unassigned_NoFeatures   7721454
Unassigned_Overlapping_Length   0
Unassigned_Ambiguity    42450
featureCounts -d 10000 -D 10 -a genrich/ATACseq/single/atac_merge.gff -o tmp.tsv -t peak -g locus_id -p bwa/Ap2oGFP1o.pb.bam

cat tmp.tsv.summary 
Status  bwa/Ap2oGFP1o.pb.bam
Assigned    3747979
Unassigned_Unmapped 0
Unassigned_Read_Type    0
Unassigned_Singleton    0
Unassigned_MappingQuality   0
Unassigned_Chimera  0
Unassigned_FragmentLength   0
Unassigned_Duplicate    0
Unassigned_MultiMapping 0
Unassigned_Secondary    0
Unassigned_NonSplit 0
Unassigned_NoFeatures   7721454
Unassigned_Overlapping_Length   0
Unassigned_Ambiguity    42450

Summary of bam file:

samtools flagstat bwa/Ap2oGFP1o.pb.bam
23008511 + 0 in total (QC-passed reads + QC-failed reads)
23008511 + 0 primary
0 + 0 secondary
0 + 0 supplementary
1391376 + 0 duplicates
1391376 + 0 primary duplicates
23008511 + 0 mapped (100.00% : N/A)
23008511 + 0 primary mapped (100.00% : N/A)
23008511 + 0 paired in sequencing
11504546 + 0 read1
11503965 + 0 read2
23008511 + 0 properly paired (100.00% : N/A)
23008511 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
subread featureCounts • 171 views
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ATpoint ★ 2.1k
@atpoint-13662
Last seen 11 hours ago
Germany

I think you additionally need -P (capital P) to trigger that the D/d options are enforced. Should be implied when using D/d but apparently it isn't.

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Yes, well spotted. Also -B is required when using -P but at least you get a meaningful error if you omit -B.

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