Hi Vickie,
If the BAM file is in coordinate order then converting to fastq will put
the read1 & read2 files in slightly different orders which will be a
problem for aligning.
You can usually convert to fastq from unsorted bam produced by the aligner
or a name sorted bam.
Best, Colin
On 20 September 2014 11:05, Vickie S <[email protected]> wrote:
> Thanks Bob for the info. A bit of distraction from samtools bug, I like to
> mention the reason I wanted to use sorting here is to allow conversion of
> bam with paired end reads to fastq. I wonder if it would lead to misleading
> fastq outpur if I convert bam to fastq without sorting the reads ? Thanks
> Collins for ur suggestion of novosort. > Subject: Re: [Samtools-help]
> [bam_sort_core] truncated file. Continue anyway > From:
> [email protected] > Date: Fri, 19 Sep 2014 22:37:40 -0400 > CC:
> [email protected] > To: [email protected] > > As I recall,
> there's some condition that the decompression library incorrectly decides
> means there's something wrong with the input file, and it returns a value
> that the calling routine can't distinguish from an end of file. The calling
> routine then reports that the file is truncated but continues to try to
> read the rest of the file, and might be successful. > > I believe I
> reported this a few months back but I really got no response from the
> samtools folks. I think/guess the basic problem is that the decompression
> library doesn't originate with this project, so there's resistance to
> making any changes to it. The change I suggested at the time *looked*
> simple enough, but it would involve a change to how that library reports
> errors. > > All that may have nothing to do with why your file isn't being
> sorted though. > > Bob H > > > On Sep 19, 2014, at 8:04 PM, Vickie S
> wrote: > >> Hi >> I am trying to sort the bam file by using the sort
> command: >> samtools sort -n aln.bam aln.qsort >> [W::sam_hdr_read]
> bgzf_check_EOF: Value too large for defined data type >> [bam_sort_core]
> truncated file. Continue anyway. >> >> I am not sure if "continue anyway"
> means it continues to sort or just aborts. >> I checked the file size. >> $
> du -hs * >> 113G aln.bam >> 8.4M aln.bam.bai >> 28K aln.qsort.bam >> >> So
> it does not seem like file is sorted. I have checked one previous thread
> about this bug but could not find any solution. Anyone comments ?
> Suggestion for any other tool ? >> >> Thanks >> >>
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