You can also try SamToFasq.jar within Picard Tools to create a Sam or Bam from
a Fastq.
N
Thumb typed for added typos
> On Sep 19, 2014, at 11:51 PM, Colin Hercus <co...@novocraft.com> wrote:
>
> 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 <is...@live.com> 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: rshar...@bx.psu.edu
>> > Date: Fri, 19 Sep 2014 22:37:40 -0400 > CC:
>> samtools-help@lists.sourceforge.net > To: is...@live.com > > 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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