bug with ISIZE numbers in .sam ?

[tba123]

bug with ISIZE numbers in .sam ?

[GoogleCodeExporter]

Hi Vladimir,

thanks for reporting this error, it looks like a bug.
Could you please extract the sequence of both mates from fastq files for
one of the problematic reads, and send them to me.
I will try to replicate the problem. Also, please let me know which genome
are you mapping to.

For a faster response, please post your questions in the STAR forum 
https://groups.google.com/d/forum/rna-star, or e-mail me directly at 
[email protected] 

Cheers
Alex

Original comment by [email protected] on 8 Apr 2014 at 6:17

• Changed state: Accepted

[GoogleCodeExporter]

Hi Alex,

thanks for your response!

this time I tested with star231o version. sorry, don't have in hand now my 
previous outputs. hope to send you later. mapping done against hg19.  

here is one problematic line in sam:
HWI-ST1149:193:C4309ACXX:5:2204:20157:21098 99  chr1    26140610    3   34S17M  =   26140585
    18446744073709551614    TGTTCTGCAGTTCCTCCAGAAGCTGGCTGGCCCTCACCTGGAGAAGTACAG @@@DDD
DABF?AFFHEGEHGFGGH@@EFHE8CFFHEDDHB;BB?DE8BF>?   NH:i:2  HI:i:2  AS:i:20 nM:i:2

here are 2 reads from input fastq files:

@HWI-ST1149:193:C4309ACXX:5:2204:20157:21098 1:N:0:GCCAAT
TGTTCTGCAGTTCCTCCAGAAGCTGGCTGGCCCTCACCTGGAGAAGTACAG
+
@@@DDDDABF?AFFHEGEHGFGGH@@EFHE8CFFHEDDHB;BB?DE8BF>?
@HWI-ST1149:193:C4309ACXX:5:2204:20157:21098 2:N:0:GCCAAT
TGGAAGCTGTACTTCTCCAGGTGAGGGCCAGCCAGCTTCTGGAGGAACTGC
+
+:=A?BDDF?DFFGIIFIFIIFFEFFFIBGEGGF?BGIIIIIGIEIIIIII

a few more examples you can find in attachment.

hope it helps.

Vladimir

Original comment by [email protected] on 9 Apr 2014 at 5:23

Attachments:

• hts.errorsams
• erroreads1.fq
• erroreads2.fq

[GoogleCodeExporter]

Dear Alex,

is there any chance to move on with this issue? Sorry to be impatient I hope 
you will have time to take a look at the problem.

Thanks.

Vladimir

Original comment by [email protected] on 15 Apr 2014 at 9:56

[GoogleCodeExporter]

Dear Alex,

your new patch (STAR_2.3.1y1) has solved the problem and now I got all my read 
counts from STAR-generated alignments with HTSeq-count without any errors.

Thanks a lot for your great job, kind and quick support!

Vladimir

Original comment by [email protected] on 17 Apr 2014 at 9:09