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,
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
> Error running cufflinks.
> return code = 1
> cufflinks: /lib64/libz.so.1: no version information available (required by
> 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
> [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
> 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
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