[mira_talk] Re: duplicate read names not allowed ?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 19 Sep 2012 10:26:18 +0100
On Wed, Sep 19, 2012 at 10:14 AM, Laurent MANCHON
<lmanchon@xxxxxxxxxxxxxx> wrote:
> Le 19/09/2012 01:55, Bastien Chevreux a écrit :
>>
>> I am inclined to say that your FASTQ is not what you expect, it may be
>> broken in some subtle way. Have a look the area around the 2241-th read and
>> hunt for things which look fishy a bit before and a bit after. I'm using
>> Heng Lis code for FASTQ parsing, which so far has probably done well with
>> billions of reads in tens of thousands of files from hundreds of people.
>>
>> B.
>
> right, i have an incorrect length of line in 2243-th read:
> +2241
> @@CFFFFFHDHHHJIIGHEIIIJIDHGDHAGGICCHGHIIJJHG>B<;@>CCC@=CBD(:A:ACCCCC@CCCCCDCCDEDD8<@CCDDD<@DDB@CBBDB
> @D61655M1:276:D10YJACXX:8:1101:11117:2032/1
> TGTAACTTCAGATTTTGTGGAATGAATCCTTAAAAACCCTTCATTGCTTATTCAGCTTCAGAAATTTCAAAGGCACATTCGGAGACGAAGTTTATTCGTT
> +2242
> CC@FFFFFHHHHHJIGIIJJJFIIGGJHIJIIJJJJJJJIIJJJJJJJJJJIJJIJIJJJJJJIJIIJJJIJJIIEHHHHHHGFFDD>BB@CDEDDEDDD
> @D61655M1:276:D10YJACXX:8:1101:11049:2038/1
> CAAGGCTTTGATGCATCGTCAGCGATGTAACCCTCGTCCTGATGCTTAGTCCACGACGGTAGGCAAATCACCCGAGTAGGGGTGCGAAAAGAGCCGGTGA
> +2243
> @<?DDDD>CF?B>9CFGG?CEAHEEHEECGECFFCHHII=9?BG@F4=C8BBGIGHIB/,6=?@ABB>@>>??=88<9::2509/1@@555<?@C9@@B&9?
> @D61655M1:276:D10YJACXX:8:1101:11065:2038/1
> CGTCATCAATGAAGAGGGCCACTTGCCAGGGGTAGGAGTGAGGGGTGGCCTCATTACCTCCAACGATGTGGGTCTCTGTCTTTGTGGGGCCACAGCCAGC
>
> Heng Lis, ah yes i know that name, i've used one of his tools named XAT, a
> cross-species alignment tool, a good and efficient tool.
> And of course BWA.
>
Heng Li's FASTQ parser is very fast, but doesn't give clear error
messages. In this case I'd much prefer an error message than
to silently data lose on input.
Peter
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