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Old 11-04-2011, 01:11 AM   #21
afaghalavi
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Location: Tehran

Join Date: Sep 2011
Posts: 5
Default Exome sequencing

Hi

We received our exome data and now i have 2 files (snps and indels) in text format.
I paste a part of that below. Please tell me what is next stage for data analysis and what shall I do ??!!!

#$ COLUMNS seq_name pos bcalls_used bcalls_filt ref Q(snp) max_gt Q(max_gt) max_gt|poly_site Q(max_gt|poly_site) A_used C_used G_used T_used
chr1 12783 2 0 G 24 AA 5 AA 5 2 0 0 0
chr1 13057 3 1 G 3 GG 4 CG 31 0 1 2 0
chr1 13351 1 0 T 1 TT 10 GT 3 0 0 1 0
chr1 14673 2 0 G 32 CC 5 CC 5 0 2 0 0

Regards
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Old 11-27-2011, 09:37 AM   #22
pd
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Location: Leuven, Belgium

Join Date: Jan 2010
Posts: 17
Default bwa sampe gives different output..

Hi all

I am trying to use sampe program from bwa with 3 options -P -s -a.. Here only -a option requires integer values to be provided. So how to specify these option in the command line because i tried it but i am getting different results.
Commands which i executed
a) bwa sampe -P -s -a 600
b) bwa sampe -Ps -a 600
c) bwa sampe -Psa 600

Here which one is correct? As all these commands are giving different results. Any suggestions?
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Old 03-22-2013, 01:09 AM   #23
azlin
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Location: selangor

Join Date: Jan 2013
Posts: 1
Red face [bwa_aln] fail to open file

hi there.
im facing a problem regarding to alignment command using bwa.

here are my command:

bwa aln -t 4 -f /media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/Alignment/R1_KS2R.sai hg19 /media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/R1_KS2R.fastq
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_seq_open] fail to open file '/media/6134b6d7-8f51-446d-9159-b10106e01d04/Postgrad/OrangAsli/KS2R/R1_KS2R.fastq'. Abort!
Aborted (core dumped)


i have no idea why it was failed to open file. anyone have suggesstion?
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