I'm trying to get the number of reads that start at a given position. I'm using bbmap pileup.sh. This is the script:
./pileup.sh in=sorted.bam basecov=coverage.txt startcov=t
How can I get coordinate information. For example, chrM 1033: 10 (so 10 reads start at that position).
Thank you
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ashafik •
Looking at inline help that command should generate the information you are looking for. Is it not doing that? I will have to test and check.
Edit: I checked this and the command should work. You will need to provide more info.
Also take a look at mosdepth (LINK) as a fast alternative.
Thanks for the reply. This is the output I get:
#RefName Pos Coverage
1 0 0
1 1 0
1 2 0
1 3 0
1 4 0
1 5 0
1 6 0
1 7 0
1 8 0
1 9 0
1 10 0
1 11 0
1 12 0
1 13 0
1 14 0
1 15 0
1 16 0
1 17 0
1 18 0
1 19 0
1 20 0
1 21 0
1 22 0
1 23 0
1 24 0
1 25 0
What do you mean by alignments? Here is the output:
MG01HX02:885:H3YW7CCX2:2:2224:20273:34465 256 1 3000472 1 33M * 0 0 TTTCCACTTGGTTGATTTCAGCTCTGAGTTTGA AJFFJAJFAFJFJFFJAAAJAFAFFJJJJJFJJ AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU NH:i:10
MG01HX02:885:H3YW7CCX2:2:2111:32299:33076 256 1 3014889 1 62M * 0 0 AGTTTGCAAGTCCAATGGGCCTCTATTTGCAGTGATGGCCGACTAGGCCATCTTTTGATACA JJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:62 YT:Z:UU NH:i:10
MG01HX02:885:H3YW7CCX2:2:2201:20953:1924 272 1 3014930 1 54M * 0 0 ACTAGGCCATCTTTTGATACATATGCAGCTAGAGACAAGAGCTCCGGGGTACTA F-JFJA7-JFFJFFA77FJ7JJJ<JJJFJFJJFJFAFJF-JJF<FJF-JJJFJJ AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:54 YT:Z:UU NH:i:10
MG01HX02:885:H3YW7CCX2:2:1118:16701:27433 256 1 3014932 1 2S64M * 0 0 AATAGGCCATCTTTTGATACATATGCAGCTAGAGACAAGAGCTCCGGGGTACTAGTTAGTTCATAT JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:-4 ZS:i:-4 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:64 YT:Z:UU NH:i:2
MG01HX02:885:H3YW7CCX2:2:1123:7101:72789 256 1 3016650 1 43M * 0 0 TATCCTTGAGAAGAGTTTTTGCTATCCTCGTTTTTTTGTTATT JJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJ AS:i:0 ZS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:43 YT:Z:UU NH:i:10
MG01HX02:885:H3YW7CCX2:2:1116:23490:48652 0 1 3018672 60 100M * 0 0 TTTTGTTTTAGGATAAAATGTTCTGTAGATATCTGTCAAGTCCATTTGTTTCATCACTTCTGTTAGTTTCACTGTGTCCCTGTTTAGTTTCTGTTTCCAT JJFJJJJJJJJFJJJJFJJJJJJFJFJJFJJJJJJJJFJFJJJJJJJJJJJJJJJJFJFJJJJJJJJJJJJFJJJJJJ<JJ<AJJJJJJJJJFJJJJJJJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UU NH:i:1
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