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,