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  • #16
    Please forgive my ignorance but do you need to use an extension on the genome file? (ie. hg18.fa instead of hg18). In the one post you show the folder contents with hg18.fa but then in the aln and sampe commands you used hg18 alone. And are the file sizes of your .sai files the right size?

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    • #17
      Hi Jon,
      I have been using hg18 for both aln and sampe step. I tried samse step also. I still get the segmentation fault.
      I have tried using bwa-0.5.6, bwa-0.5.7 as well as from svn...

      In the very firts step to convert solexa to fastq format,

      maq-0.7.1/maq sol2sanger s_5_2_sequence.txt s_5_2_fastq.txt
      Does it contain any bug which is causing this problem? Thanks.
      Last edited by seq_GA; 06-07-2010, 07:02 PM.

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      • #18
        problem with BWA

        I used BWA for indexing hg19, but I had the below error !!!

        afagh@afagh-VirtualBox:~$ bwa index -a bwtsw -p hg19 /mnt/desktop/hg19.fa
        [bwa_index] Pack FASTA... 169.44 sec
        [bwa_index] Reverse the packed sequence... Killed


        Please, help me

        Thank you

        Comment


        • #19
          Originally posted by afaghalavi View Post
          I used BWA for indexing hg19, but I had the below error !!!

          afagh@afagh-VirtualBox:~$ bwa index -a bwtsw -p hg19 /mnt/desktop/hg19.fa
          [bwa_index] Pack FASTA... 169.44 sec
          [bwa_index] Reverse the packed sequence... Killed


          Please, help me

          Thank you
          I once observed the same error when running bwa in a Virtual Box - Linux. No idea why. It should work if you use a non-virtual system.

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          • #20
            Thank you so much

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            • #21
              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


              Best

              Afagh

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              • #22
                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

                Comment


                • #23
                  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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                  • #24
                    [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?

                    Comment

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