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Old 03-23-2012, 09:29 AM   #1
Patidar
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Default SOLid2fastq

Hi,
I ran solid2fastq from bfast+bwa and from bfast.
the stats are different for a sample i.e. entirely different:

/usr/local/bfast+bwa/bin/solid2fastq -o khan03_20101013_PE_NB1001WGA_E /home/rajehh/mapping/data/DW/khan03_20101013_PE/khan03_20101013_PE_NB1001WGA_E_F*.csfasta /home/rajehh/mapping/data/DW/khan03_20101013_PE/khan03_20101013_PE_NB1001WGA_E_F*.qual
Outputting, currently on:
105443471
Found
number_of_ends number_of_reads
1 105301151
2 142320


[rajehh@biowulf test]$ /usr/local/bfast/bin/solid2fastq -o NB1001WGA_E /home/rajehh/mapping/data/DW/khan03_20101013_PE/khan03_20101013_PE_NB1001WGA_E_F*.csfasta /home/rajehh/mapping/data/DW/khan03_20101013_PE/khan03_20101013_PE_NB1001WGA_E_F*.qual
Outputting, currently on:
105443471
Found
number_of_ends number_of_reads
1 0
2 105443471

Any Idea why the two converters do not give the same result ?

Thanks.
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Old 03-23-2012, 02:14 PM   #2
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Very interesting. Could you share the data (or reduce it to manageable size)?
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Old 03-23-2012, 04:04 PM   #3
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Question

Hi Nils,
I got it to 5000 Reads/file and
/usr/local/bfast+bwa/bin/solid2fastq F3 F5 F3.q F5.q
is
Found
number_of_ends number_of_reads
1 4999
2 0
/usr/local/bfast/bin/solid2fastq F3 F5 F3.q F5.q
is

Found
number_of_ends number_of_reads
1 0
2 4999


But the file size it over 1MB and I cant attache it here.

If you would like to see them I can send in a mail.

Thanks for help
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Old 03-23-2012, 04:25 PM   #4
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Please send it to bfast-help@lists.sourceforge.net
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Old 03-23-2012, 04:37 PM   #5
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I sent it to you using secure mail.

Thanks for the help.
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Old 03-26-2012, 05:33 AM   #6
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Hi Nils,

If I am correct you received my mail. Did you got any chance to look into this matter?

Thanks.
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Old 03-26-2012, 06:36 AM   #7
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Hi,

For another sample I noticed:

Found
number_of_ends number_of_reads
1 0
2 173685356

Collecting paired end statistics...
Collected statistics for 0 paired end distances.
The paired end distance range was from 2147483647 to -2147483648.
The paired end distance mean and standard deviation were 200.00 and 150.00. (Specified.)
Reads processed: 10000000
************************************************************
Alignment complete.
************************************************************
Found 1416266 reads with no ends mapped.
Found 8583734 reads with 1 end mapped.
Found 8583734 reads with at least one end mapping.


Am I doing something wrong ?

My commands are
SOLID2FASTQ
/usr/local/bfast/bin/solid2fastq -n 10000000 -o sample F3 F5 F3.qual F5.qual

MATCH
$bfast match -f $ref -A 1 -n 16 -t -T $workdir/tmp/ -r $workdir/$_ >$workdir/$_.bmf

LOCALALIGN
$bfast localalign -f $ref -A 1 -n 16 -t -m $workdir/$_.bmf >$workdir/$_.baf

POSTPROCESS

$bfast postprocess -f $ref -A 1 -n 16 -a 3 -Y 0 -t -r $workdir/rg_info_$SAMPLE -v 200 -s 150 -i $workdir/$_.baf >$workdir/$_.1.sam

I am aligning it to the hg19.


Thanks,
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Old 03-26-2012, 07:41 AM   #8
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Quote:
Originally Posted by Patidar View Post
Hi Nils,

If I am correct you received my mail. Did you got any chance to look into this matter?

Thanks.
No, I am doing this on my own time, so I may not be able to look at it in the short term. I would be happy to accept a patch if you solve it before I do.
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Old 03-26-2012, 08:15 AM   #9
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Hi Nils,

Thanks for looking into it.

Any Idea on the 9th post in this thread ?
"
The paired end distance range was from 2147483647 to -2147483648.
The paired end distance mean and standard deviation were 200.00 and 150.00. (Specified.)
"

is "2147483647 to -2147483648." is the default range ?
I looked into the Sam files and they looks good to me.
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