filterbarcodes creates duplicated bam lines #76
Description
I used the following code to subset a single-cell bam from a 10X Multiome ATAC bam file:
sinto filterbarcodes --bam atac_possorted_bam.bam --cells GTGATCAGTTGAGCCG-1.txt --outdir . --nproc 12
However, grep LH00328:406:22GHLYLT4:2:2404:37243:13079 on subset bam file gives:
LH00328:406:22GHLYLT4:2:2404:37243:13079 65 chr16 58735131 60 150M chr2 32916362 0 AAACTCGTGTATGTCAAATCCTGATAACTGTTTGTGGAAGGAAATGAATCGGTTTTGAAGGAAATGAATCGGTTTTAAAGGAAAAAGCAAATGAATTTCAGACACATCCACAAGTCAAACGAGTCTTTCTCATGTGTAGTCTATTTCTCT -II9III-IIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIII9II-II9IIIIIIIIIIIIIIIIII-IIIIIII9I99IIII9IIIIIIIIIIIIIIIIIII9IIIII9II9III9IIIII9I NM:i:0 MD:Z:150 AS:i:150 XS:i:21 CR:Z:TCCTGATCAGCAACTT CY:Z:9III9I9I--I-9-I- CB:Z:GTGATCAGTTGAGCCG-1 BC:Z:GGCGGAAT QT:Z:9IIIII9I RG:Z:S2_PGT_pool4:MissingLibrary:1:22GHLYLT4:2
LH00328:406:22GHLYLT4:2:2404:37243:13079 65 chr16 58735131 60 150M chr2 32916362 0 AAACTCGTGTATGTCAAATCCTGATAACTGTTTGTGGAAGGAAATGAATCGGTTTTGAAGGAAATGAATCGGTTTTAAAGGAAAAAGCAAATGAATTTCAGACACATCCACAAGTCAAACGAGTCTTTCTCATGTGTAGTCTATTTCTCT -II9III-IIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIII9II-II9IIIIIIIIIIIIIIIIII-IIIIIII9I99IIII9IIIIIIIIIIIIIIIIIII9IIIII9II9III9IIIII9I NM:i:0 MD:Z:150 AS:i:150 XS:i:21 CR:Z:TCCTGATCAGCAACTT CY:Z:9III9I9I--I-9-I- CB:Z:GTGATCAGTTGAGCCG-1 BC:Z:GGCGGAAT QT:Z:9IIIII9I RG:Z:S2_PGT_pool4:MissingLibrary:1:22GHLYLT4:2
LH00328:406:22GHLYLT4:2:2404:37243:13079 129 chr2 32916362 0 51M99S chr16 58735131 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGAGGGGGGGGGGGAGAGAGAGCGGATAGGTATGGTAACAAGGAGGGAGTGCAGTAGCGCAGTCCTGGCTCACTGCAATGTTTTTTTTTTTTTTTTTTTTTTTTTGGTTGGGG -9I9II9999IIIII9I99II999II9-99--999-99--999-99--9---9---------9-9-----9-------9---99-9-9-II--9I999-I--9I9-9-9-9--I-9-9--99-99I9---99-99-99III--9I-II-I NM:i:1 MD:Z:27G23 AS:i:46 XS:i:46 SA:Z:chr16,58735808,-,14S54M82S,0,3; CR:Z:TCCTGATCAGCAACTT CY:Z:9III9I9I--I-9-I- CB:Z:GTGATCAGTTGAGCCG-1 BC:Z:GGCGGAAT QT:Z:9IIIII9I RG:Z:S2_PGT_pool4:MissingLibrary:1:22GHLYLT4:2
Line 1 and 2 are completely the same. The same grep command on the original atac_possorted_bam.bam only gives:
LH00328:406:22GHLYLT4:2:2404:37243:13079 65 chr16 58735131 60 150M chr2 32916362 0 AAACTCGTGTATGTCAAATCCTGATAACTGTTTGTGGAAGGAAATGAATCGGTTTTGAAGGAAATGAATCGGTTTTAAAGGAAAAAGCAAATGAATTTCAGACACATCCACAAGTCAAACGAGTCTTTCTCATGTGTAGTCTATTTCTCT -II9III-IIIIIII9IIIIIIIIIII9IIIIIIIIIIIIIIII9IIIIIIIII9IIIIIIIIIIIII9II-II9IIIIIIIIIIIIIIIIII-IIIIIII9I99IIII9IIIIIIIIIIIIIIIIIII9IIIII9II9III9IIIII9I NM:i:0 MD:Z:150 AS:i:150 XS:i:21 CR:Z:TCCTGATCAGCAACTT CY:Z:9III9I9I--I-9-I- CB:Z:GTGATCAGTTGAGCCG-1 BC:Z:GGCGGAAT QT:Z:9IIIII9I RG:Z:S2_PGT_pool4:MissingLibrary:1:22GHLYLT4:2
LH00328:406:22GHLYLT4:2:2404:37243:13079 129 chr2 32916362 0 51M99S chr16 58735131 0 GGGGGGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGAGGGGGGGGGGGAGAGAGAGCGGATAGGTATGGTAACAAGGAGGGAGTGCAGTAGCGCAGTCCTGGCTCACTGCAATGTTTTTTTTTTTTTTTTTTTTTTTTTGGTTGGGG -9I9II9999IIIII9I99II999II9-99--999-99--999-99--9---9---------9-9-----9-------9---99-9-9-II--9I999-I--9I9-9-9-9--I-9-9--99-99I9---99-99-99III--9I-II-I NM:i:1 MD:Z:27G23 AS:i:46 XS:i:46 SA:Z:chr16,58735808,-,14S54M82S,0,3; CR:Z:TCCTGATCAGCAACTT CY:Z:9III9I9I--I-9-I- CB:Z:GTGATCAGTTGAGCCG-1 BC:Z:GGCGGAAT QT:Z:9IIIII9I RG:Z:S2_PGT_pool4:MissingLibrary:1:22GHLYLT4:2
The original bam file is too large to upload but if you need anything to diagnose I would be happy to help.