I have a small sample of records from a bam file. I obtained them by intersecting with a bed file not enforcing strand-specificity. So I get them all back upon performing the same intersection again:
$ bedtools intersect -a sample.bam -b features.bed -wa -u -f 1.0 | samtools view
MN00481:17:000H2FH5N:1:11104:12480:15984 16 III 4499483 42 28M * 0 0 CAGGAACACGCACATCGTCGATTTTCAG FFFFFAFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YT:Z:UU
MN00481:17:000H2FH5N:1:11103:9925:11522 16 IV 2388448 42 30M * 0 0 CACTGGAACTGGTCCGATCTTCAAGCCGGT FFFFFFFFFFA/FFFFAFFFFFF/FFAFAF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
MN00481:17:000H2FH5N:1:22109:11939:5243 16 IV 4749336 42 29M * 0 0 ATGTGGATGCGGTCAGCTTGGGCACGATG FFFFFFFFFFFF/FFFF6FFFFFFFF/FF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:29 YT:Z:UU
MN00481:17:000H2FH5N:1:22104:17385:19431 16 V 4443064 42 29M * 0 0 CAAAATGTGAACAGGAACGTTTTCATGAG F/FFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:29 YT:Z:UU
MN00481:17:000H2FH5N:1:23105:22058:12968 0 X 981524 42 29M * 0 0 CCATCGATTCTCATTTTAATGCTGGTGCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:29 YT:Z:UU
MN00481:17:000H2FH5N:1:12104:7867:7500 16 X 4214381 42 29M * 0 0 GCTGCAGGAATGACGGCTCTAGCAAACGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:29 YT:Z:UU
Now I would like to enforce strand-specificity, but in either case, none of the records pass the filter:
Same strand (-s
):
$ bedtools intersect -a sample.bam -b features.bed -wa -u -f 1.0 -s | samtools view
$ # nothing here
Opposite strand (-S
):
$ bedtools intersect -a sample.bam -b features.bed -wa -u -f 1.0 -S | samtools view
$ # nothing here
What is the correct way of doing this?
Edit
Bedtools version:
$ bedtools --version
bedtools v2.27.1
My bed file has strand information:
$ tail features.bed
X 17617826 17619458 "WBGene00015867" + .
X 17622777 17640743 "WBGene00019211" - .
X 17650177 17651594 "WBGene00044771" + .
X 17662457 17665357 "WBGene00003744" + .
X 17671028 17680790 "WBGene00020732" + .
X 17680910 17682294 "WBGene00044772" - .
X 17695231 17701744 "WBGene00017625" + .
X 17710485 17711674 "WBGene00019189" - .
X 17714455 17714832 "WBGene00007069" + .
X 17714967 17718717 "WBGene00007068" + .