missing avg_distance_to_effective_3p_end
stemangiola opened this issue · 0 comments
stemangiola commented
In analysis some BAM files I get these kind of results (one line shown)
chr17
748892
T
1
=:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
T:1:0.00:37.00:0.00:1:0:0.00:0.00:0.00:0:0.00:0.00:0.00
N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
Apparently none of the key info to use for example sinvict are present.
Is this a pathological result?
I aligned the reads with bwa
M04416:61:000000000-C2G5K:1:1101:20297:9269 77 * 0 0 * * 0 0 GAGGGGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATG >1>A1>AAFFFFFAFFGAGGFFDFAGHGHHGCCEEEGGHFHGHHFA11F1GFFF0F?FEAFFAGHHHFHHGHBGFH0/GGEEGGEGEBHHH/FF@?EACHCC/B?FGHH2?GGB1FFB2FBGHHBGHHFHGGGGGHHGHFHHFGHBGGHHH AS:i:0 XS:i:0
M04416:61:000000000-C2G5K:1:1101:20297:9269 141 * 0 0 * * 0 0 CAGCGGCAGACTTGCCACCAAGTCCAACCAAATCAAGCAACTTATCAGAAACGGCAGAAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGGACGGCCTCATCAGGGTTAGG A1>AA?@DDAFFGGGGGGG00BGFHH1BAFGGFD1AAF0FGFGFFGHHHHCGGECECGBGHDFHFEAEHHHHHG@CGEGDF@D1B1FHHHBGGHGHBGBE>FHBEGHHHH1>FGHHFFHHHGGHHHGHFHHGGGGGGGHHHHHHGHGHHHG AS:i:0 XS:i:0
M04416:61:000000000-C2G5K:1:1101:12893:9276 83 chr17 10123357 60 8S66M11S = 10123357 -66 CCCCCTCCTCTGTTGCTGCTGGTCCAGGGACCACACTTTAAGAAGCCCTACCCTAGAATCTGAAGGTTGGAAAGCCATAGGATTC GGGGFHGHHHHHHGHHHHHHHHHHHHHIHHGHHHGHHHHHHHHHHGGGHHGHHHHHHHHHHHHGGGGGGGGGGCFFFFFFCCBBB NM:i:1 MD:Z:58C7 AS:i:61 XS:i:31
M04416:61:000000000-C2G5K:1:1101:12893:9276 163 chr17 10123357 60 8S66M11S = 10123357 66 CCCCCTCCTCTGTTGCTGCTGGTCCAGGGACCACACTTTAAGAAGCCCTACCCTAGAATCTGAAGGTTGGAAAGCCATAGGATTC ABCCCCCCFFFFGGGGGGGGGGGHHHGHGGGGHHHGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHHGHHHHGHHHHHHHHHH NM:i:1 MD:Z:58C7 AS:i:61 XS:i:31
What is the best command to align the reads before using bam-readcount?
Thanks