Entering edit mode
2.2 years ago
irem
•
0
Hello,
I'm trying to find the strand information of my bam samples. But I encounter the following error:
Reading reference gene model Homo_sapiens.GRCh38.79_new.bed ... Done
Loading SAM/BAM file ... Total 200000 usable reads were sampled
Unknown Data type
Could you please help me to find the error here? Thanks a lot!
Bam files look like that:
samtools view RNA_S4666Nr1.sorted.dedup.bam |head
A01144:239:HVVFNDSX2:1:2445:12292:25347 99 1 14467 255 101M = 14617 248 GGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTG FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:191 nM:i:3 MQ:i:255 MC:Z:98M ms:i:3565
A01144:239:HVVFNDSX2:2:1162:18168:32299 99 1 14467 255 1S100M = 14639 273 GGGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:193 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3553
A01144:239:HVVFNDSX2:2:2453:9561:7717 99 1 14467 255 101M = 14647 281 GGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:194 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3554
A01144:239:HVVFNDSX2:3:2361:24487:35665 99 1 14467 255 101M = 14650 284 GGCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:194 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3688
A01144:239:HVVFNDSX2:3:2423:27335:16360 99 1 14468 255 101M = 14688 321 GCGCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:194 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3700
A01144:239:HVVFNDSX2:3:1435:8675:12164 99 1 14470 255 101M = 14632 263 GCAGGCTGGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:194 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3431
A01144:239:HVVFNDSX2:3:1565:24858:25974 99 1 14477 255 101M = 14695 319 GGGTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCACCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCAC FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:194 nM:i:3 MQ:i:255 MC:Z:101M ms:i:3688
A01144:239:HVVFNDSX2:1:1350:9851:19711 99 1 14479 255 99M = 14607 229 GTGGAGCCGTCCCCCCATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAAGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:198 nM:i:0 MQ:i:255 MC:Z:101M ms:i:3725
A01144:239:HVVFNDSX2:1:1130:6958:24189 99 1 14495 255 101M = 14641 247 ATGGAGCACAGGCAGACAGAAGTCCCCGCCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCACAGTGCTGGTTCCGTCACC FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:190 nM:i:5 MQ:i:255 MC:Z:101M ms:i:3271
A01144:239:HVVFNDSX2:2:2669:1479:27539 99 1 14518 255 100M = 14688 271 CCCCGCCCCAGCTGTGTGGCCTCAGGCCAGCCTTCCGCTCCTTGAAGCTGGTCTCCGCACAGTGCTGGTTCCGTCACCCCCACCCAGGGAAGCAGGTCTG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF NH:i:1 HI:i:1 AS:i:189 nM:i:5 MQ:i:255 MC:Z:101M ms:i:3688
And the bed file looks like:
Homo_sapiens.GRCh38.79.bed | head
1 11868 14409 ENST00000456328 0 + 11868 14409 0 3 359,109,1189, 0,744,1352,
1 12009 13670 ENST00000450305 0 + 12009 13670 0 6 48,49,85,78,154,218, 0,169,603,965,1211,1443,
1 17368 17436 ENST00000619216 0 - 17368 17436 0 1 68, 0,
1 14403 29570 ENST00000488147 0 - 14403 29570 0 11 98,34,152,159,198,136,137,147,99,154,37, 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
1 29553 31097 ENST00000473358 0 + 29553 31097 0 3 486,104,122, 0,1010,1422,
1 30266 31109 ENST00000469289 0 + 30266 31109 0 2 401,134, 0,709,
1 30365 30503 ENST00000607096 0 + 30365 30503 0 1 138, 0,
1 34553 36081 ENST00000417324 0 - 34553 36081 0 3 621,205,361, 0,723,1167,
1 35244 36073 ENST00000461467 0 - 35244 36073 0 2 237,353, 0,476,
1 52472 53312 ENST00000606857 0 + 52472 53312 0 1 840, 0,
