Hi Carlos,
I had finally found a workaround by selecting header line matching ^@ and
merging this with the SAM file. but I think your solution is far more
elegant. I'll try.
Thanks

2012/2/28 Carlos Borroto <carlos.borr...@gmail.com>

> Hi Denis,
>
> In a similar situation I was able to move forward using NGS: Picard
> (beta) / Replace SAM/BAM Header to copy back the header from the
> original unfiltered BAM or SAM file.
>
> Hope it helps,
> Carlos
>
> On Tue, Feb 28, 2012 at 3:15 PM, denis puthier <puth...@tagc.univ-mrs.fr>
> wrote:
> > Dear All,
> > I would like to add some filtering steps in my RNA-Seq pipeline. To do
> so, I
> > used the accepted.hits from TopHat and apply a filter using  NGS: SAM
> Tools
> >> Filter SAM and select reads with bitwise flag 0x0002. This does the job.
> > However, I am unable to use cufflink after this step and got the
> following
> > error message that seems to indicate that the file contains no header
> and is
> > unsorted. Is there a workaround ?
> > Thanks a lot
> >
> > http://main.g2.bx.psu.edu/u/dputhier/h/srx011549
> >
> >
> > Error running cufflinks.
> > return code = 1
> > cufflinks: /lib64/libz.so.1: no version information available (required
> by
> > cufflinks)
> > Command line:
> > cufflinks -q --no-update-check -s 20 -I 300000 -F 0.100000 -j 0.150000
> -p 8
> > -m 200 -g /galaxy/main_pool/pool5/files/003/858/dataset_3858145.dat
> > /galaxy/main_pool/pool1/files/003/858/dataset_3858306.dat
> > [bam_header_read] EOF marker is absent.
> > [bam_header_read] invalid BAM binary header (this is not a BAM file).
> > File /galaxy/main_pool/pool1/files/003/858/dataset_3858306.dat doesn't
> > appear to be a valid BAM file, trying SAM...
> > [14:11:28] Loading reference annotation.
> > [14:11:28] Inspecting reads and determining fragment length distribution.
> >
> > Error: this SAM file doesn't appear to be correctly sorted!
> >         current hit is at chr10:181061, last one was at chr1:245006405
> > Cufflinks requires that if your file has SQ records in
> > the SAM header that they appear in the same order as the chromosomes
> names
> > in the alignments.
> > If there are no SQ records in the header, or if the header is missing,
> > the alignments must be sorted lexicographically by chromsome
> > name and by position.
> >
> >
> > --
> > ====================================================================
> > Denis Puthier
> > laboratoire INSERM
> > TAGC/INSERM U928
> > Parc Scientifique de Luminy case 928
> > 163, avenue de Luminy
> > 13288 MARSEILLE cedex 09
> > FRANCE
> > Mail: puth...@tagc.univ-mrs.fr
> > Tel: (National) 04 91 82 87 11 / (International) 33 4 91 82 87 11
> > Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01
> >
> > Web:
> > http://tagc.univ-mrs.fr/puthier
> > http://biologie.univ-mrs.fr/view-data.php?id=245
> > http://tagc.univ-mrs.fr/tbrowser
> > ====================================================================
> >
> > ___________________________________________________________
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> ___________________________________________________________
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-- 
====================================================================
Denis Puthier
laboratoire INSERM
TAGC/INSERM U928
Parc Scientifique de Luminy case 928
163, avenue de Luminy
13288 MARSEILLE cedex 09
FRANCE
Mail: puth...@tagc.univ-mrs.fr
Tel: (National) 04 91 82 87 11 / (International) 33 4 91 82 87 11
Fax: (National) 04 91 82 87 01 / (International) 33 4 91 82 87 01

Web:
http://tagc.univ-mrs.fr/puthier
http://biologie.univ-mrs.fr/view-data.php?id=245
http://tagc.univ-mrs.fr/tbrowser
====================================================================
___________________________________________________________
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