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2.7 years ago
bill
•
0
My BAM file seems to be missing information on cell barcodes. I find that each BAM file represents the sequencing result of a cell.
Here's what I found when I combined dozens of BAM files.
Can someone tell me how to find the cell barcode? Thanks.
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:1114:17527:80767 163 chr1 10514 35 50M = 10518 54 GAACTGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGACAAC CBCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGF MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-15 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-19E18592
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:1114:17527:80767 83 chr1 10518 35 50M = 10514 -54 TGTGCTCCGCCTTCAGAGTACCACCGAAATCTGTGCAGAGGACAACGCAG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBBB@A MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-15 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-19E18592
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:1306:9729:13815 163 chr1 64595 30 50M = 64632 87 CATGTATACATATGTAACTAACCTGCACATTGTGCACATGTACCCTAGAA CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-FB16E09
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:1306:9729:13815 83 chr1 64632 30 50M = 64595 -87 ATGTACCCTAGAACTTAAAGTATAATAAAAAAAAATAGACTCTAGTACTC CEGGGGGGGGGGGGFGGGGGGGGGGGGGGGGEGGGGGGGGGCGFF@0>3? MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-8 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-FB16E09
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2216:4692:2332 99 chr1 134987 30 50M = 135006 69 CCAAGAGGCTGCCGGAAGGGAAAAACAGGGCCTGGAATGGCCGACGTGAG ?BB@BGEGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGG MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-19E18592
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2216:4692:2332 147 chr1 135006 30 50M = 134987 -69 GAAAAACAGGGCCTGGAATGGCCGACGTGAGGAATGAGCTGGGCCTAAAG GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGCCCCC MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-19E18592
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2306:20796:20526 163 chr1 174391 30 50M = 174396 55 TGGTGGTTCATGCCTGTAATTCCAACAGTTTGGGAGGCCAAGGCAGGCAG CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-5B8600F3
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2306:20796:20526 83 chr1 174396 30 50M = 174391 -55 GTTCATGCCTGTAATTCCAACAGTTTGGGAGGCCAAGGCAGGCAGATAAC GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBB><3 MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-5B8600F3
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2106:1872:81343 163 chr1 244109 30 50M = 244123 64 CTATAAACATGTAGCATTGTGATTAGGGCTGGTTCTCCTTCTAGAGATAT BCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-1F23889B
D00829_0139_ACC51WANXX_PEdi_MB67-MB74:2:2106:1872:81343 83 chr1 244123 30 50M = 244109 -64 CATTGTGATTAGGGCTGGTTCTCCTTCTAGAGATATGGTAGGATTGCAAT GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGBBB@B MD:Z:50 XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:-5 YS:i:0 YT:Z:CP PG:Z:MarkDuplicates-1F23889B
This questions lacks any context of the experiment and commands you ran. What are these data?
These are the single-cell ATAC-seq data, which I downloaded from someone else's published data. I didn't do anything with the data