Re: [Bio-bwa-help] total noob at bwa

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And, if the sequences are whole genomes or whole chromosomes, rather than short sequences like reads, genes, or ESTs, you may want to consider a whole genome aligner, such as Mauve (http://asap.ahabs.wisc.edu/mauve/index.php).  I'm sure there are many others as well.

Michael

-----Original Message-----
From: Tom Blackwell [mailto:tb...@um...]
Sent: Monday, November 22, 2010 8:32 AM
To: Jillian Rowe
Cc: bio...@li...
Subject: Re: [Bio-bwa-help] total noob at bwa. .

Jillian  -

Guessing from the file names, I think the objective is
to identify sequence-similar regions between human and
cow genome reference sequences from a particular region.

NCBI Blast is probably a better tool for doing this than
bwa.  I would start by using the web service available at
http://blast.ncbi.nlm.nih.gov/Blast.cgi .  For this purpose,
I would skip the top two headings in that page and start
under the heading "Specialized BLAST" with the 9th entry
under that heading:  "Align two (or more) sequences using
BLAST (bl2seq)".  This takes you to a page where you can
upload your two .fasta files, then choose search parameters
and run the search.  For cross species comparisons, one
wants either "More dissimilar sequences (discontinuous
megablast)" or "Somewhat similar sequences (blastn)".
These are choices under "Optimize for".  Technical details
are shown under "Choose a BLAST algorithm ?" >> "more..."
just below the three "Optimize for" options.

                                        -  tom blackwell  -

On Sun, 21 Nov 2010, Jillian Rowe wrote:

> Hello there,
>
> I am very, very new at using BWA, and a linux environment in general. I
> have bwa 0.5.8c installed on a Ubuntu 10.04 OS. I really can't stress
> enough how new I am at this.
>
> I'm completely lost. I can't find a complete beginners guide with sample
> code. Pretty much what I am trying to do is align 2 fasta sequences.
>
> homotaysachs.fasta
> bostaurustaysachs.fasta
>
> I wrote up a bash file that looks like this:
> #!/bin/bash
>
> bwa index -a bwtsw homotaysachs.fasta
>
> bwa aln homotaysachs.fasta bostaurustaysachs.fasta > aln_sa.sai
>
> bwa samse homotaysachs.fasta aln_sa.sai bostaurustaysachs.fasta >
> aln_sa.sai
>
> bwa sampe homotaysachs.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq >
> aln.sam
>
> bwa bwasw homotaysachs.fasta long_read.fastq > aln.sam
>
> When I run it I get:
>
> root@jill-desktop:/home/jill/bwa-0.5.8c/Run# bash taysachs.sh
> [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
> [bwt_restore_bwt] fail to open file 'homotaysachs.fasta.bwt'. Abort!
> taysachs.sh: line 3:  2969 Aborted                 bwa aln
> homotaysachs.fasta bostaurustaysachs.fasta out.sai
> root@jill-desktop:/home/jill/bwa-0.5.8c/Run# bash taysachs.sh
> [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
> [bwt_restore_bwt] fail to open file 'homotaysachs.db.fasta.bwt'. Abort!
> taysachs.sh: line 3:  3003 Aborted                 bwa aln
> homotaysachs.db.fasta bostaurustaysachs.fasta out.sai
> root@jill-desktop:/home/jill/bwa-0.5.8c/Run# bash taysachs.sh
> [bwa_index] Pack FASTA... 0.00 sec
> [bwa_index] Reverse the packed sequence... 0.00 sec
> [bwa_index] Construct BWT for the packed sequence...
> BWTIncConstruct() : Not enough memory allocated!
> [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
> [bwt_restore_bwt] fail to open file 'homotaysachs.fasta.bwt'. Abort!
> taysachs.sh: line 9:  3076 Aborted                 bwa aln
> homotaysachs.fasta bostaurustaysachs.fasta > aln_sa.sai
> [bwa_read_seq] 0.0% bases are trimmed.
> [bwa_aln_core] convert to sequence coordinate... [bwt_restore_bwt] fail
> to open file 'homotaysachs.fasta.bwt'. Abort!
> taysachs.sh: line 13:  3077 Aborted                 bwa samse
> homotaysachs.fasta aln_sa.sai bostaurustaysachs.fasta > aln_sa.sai
> [bwa_seq_open] fail to open file 'read1.fq'. Abort!
> taysachs.sh: line 17:  3078 Aborted                 bwa sampe
> homotaysachs.fasta aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln.sam
> [bwt_restore_bwt] fail to open file 'homotaysachs.fasta.bwt'. Abort!
> taysachs.sh: line 21:  3079 Aborted                 bwa bwasw
> homotaysachs.fasta long_read.fastq > aln.sam
> root@jill-desktop:/home/jill/bwa-0.5.8c/Run#
>
> Help would be so, so appreciated. So would pointing me in the direction
> of some good resources.
>
> Thanks!
>

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