Hi Tom, thanks a lot for the suggestion. It works! Sean
> Date: Thu, 26 Mar 2015 13:14:38 +0000
> From: tbla...@umich.edu
> To: ying_c...@live.com
> CC: samtools-help@lists.sourceforge.net
> Subject: Re: [Samtools-help] samtools split output filename format string
> error
>
>
> Perhaps this is a quoting issue. I would try putting single quotes around
> the -f format string in the cammand line, rather than double quotes.
>
> - tom blackwell -
>
> On Thu, 26 Mar 2015, ying chen wrote:
>
> > Hi,
> >
> > I am trying to use samtools split command to split my bam file into small
> > bam files by read group. The input bam files are the CCLE RNASeq bams.
> > It worked when I did
> >
> > samtools split -u G20486.Calu-1.2_noRG.bam -f "%*_%#.bam" -v
> > G20486.Calu-1.2.bam
> > It generated bam files with suchs as G20486.Calu-1.2_0.bam,
> > G20486.Calu-1.2_1.bam, ...
> > Then I tried to add RG id into resulting bam file names by
> > samtools split -u G20486.Calu-1.2_noRG.bam -f "%*_%!_%#.bam" -v
> > G20486.Calu-1.2.bam
> > and I got the error message:
> > bash: !_%#.bam: event not found
> > It seems that samtools split has trouble identifying RG ID. I tried and
> > could not find much info or documentation regarding samtools split except
> > the samtools help split.
> > Here are the bam file itself:
> > samtools view G20486.Calu-1.2.bam | more
> > C0UNPACXX120727:2:1207:1813:5925 419 1 11615 1 101M
> > = 11780 266 TAGGAATG
> > CCTGTTTCTCCACAAAGTGTTTACTTTTGGATTTTTGCCAGTCTAACAGGTGAAGCCCTGGAGATTCTTATTAGTGATTTGGGCTGGGGCCTG
> > <@@DFFFDDDFHBHII
> > G4I@?FCEHHFFBGEEHI@HDGCD@GFFG@GEGGBHHIBFHDIICHHG>@GHIDD7=A)?EHHFF:@>CFCCCE6?ABD<=/;5?
> > CC:Z:15 PG:Z:tophat.D
> > RG:Z:C0UNP.2 NH:i:3 HI:i:0 NM:i:0 CP:i:102519455 MQ:i:1 UQ:i:0
> > C0UNPACXX120727:5:2214:18693:14398 163 1 11615 1 101M
> > = 11780 266 TAGGAATG
> > CCTGTTTCTCAACAAAGTGTTTACTTTTGGATTTTTGCCAGTCTAACAGGTGAAGCCCTGGAGATTCTTATTAGTGATTTGGGCTGGGGCCTG
> > ?@@DD>DAAF4AAEFH
> > EF,<<CF;FAFAC?HCC<CGHA*:CDH>DCHFHHEDBH?8DH8CFIJIIG;6;(@E>EFEE>=@BC;@>>A##############
> > CC:Z:15 PG:Z:tophat.8 RG:Z:C0UNP.5 NH:i:3 HI:i:0 NM:i:1
> > CP:i:102519455 MQ:i:1 UQ:i:11
> >
> Any help would be greatly appreciated!
> >
> >
> Best regards,
> >
> > Sean
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