Hi all,
once again I have to ask for your help, since I couldn't find any thread on the board that is reflecting my problem.
First of all: I use artificially created single end reads in Illumina FASTQ format that look like the following (the quality values are not as yet of any concern, that is why it's h):
To get used to BWA (I used bowtie before and that works fine with the data), I'm aligning them against a small part of the genome (the one I used to create them is included) which consists of several FASTA entries of exons, so basically:
So far I've tried
w/ and w/o the -I flag set, and after that:
It produces a SAM file that looks like this (independent of the -I flag):
I tried to get some information out of this but couldn't find anything comparable on the web or the manuals so far. So to make it short: I have no clue what to do with that file and why it looks like it does, since the once described elsewhere look completely different, as far as I can tell.
Any help is much appreciated, thanks in advance.
Regards
once again I have to ask for your help, since I couldn't find any thread on the board that is reflecting my problem.
First of all: I use artificially created single end reads in Illumina FASTQ format that look like the following (the quality values are not as yet of any concern, that is why it's h):
@Identifier1:1:1:1:1#NNNNNN/1
ACAATGTTTCTCATGCTCCAGTGAT
+Identifier1:1:1:1:1#NNNNNN/1
hhhhhhhhhhhhhhhhhhhhhhhhh
@Identifier2:1:2:1:1#NNNNNN/1
TTTCCTCATCTACAACAGTGATTGG
+Identifier2:1:2:1:1#NNNNNN/1
hhhhhhhhhhhhhhhhhhhhhhhhh
ACAATGTTTCTCATGCTCCAGTGAT
+Identifier1:1:1:1:1#NNNNNN/1
hhhhhhhhhhhhhhhhhhhhhhhhh
@Identifier2:1:2:1:1#NNNNNN/1
TTTCCTCATCTACAACAGTGATTGG
+Identifier2:1:2:1:1#NNNNNN/1
hhhhhhhhhhhhhhhhhhhhhhhhh
>RefIdentifier1
ACAATGTTTTTGATCTCTTTAACCTCATCTACCTCAGGCAACAATGTTTT
TGATCTCTTTAACCTCATCTACCTCAGGCAGTGCTCATGGTGATTTGTG
CTCATGGTGATTT
>RefIdentifier2
CATCTACCTCAGGCAACCTCATGGTATTTGTGCTCATGGTGATTCCCTA
TCTACTTTTGAACAATGTTTTTGATCTCTTTAACCTTCTCTTTAACCTCCT
CAGGCAGTGGATGATGACTGACTGACTGTTTGATCGTGACTGATCGTG
ATCTTTTTTACGGGACATTAAAAGGCGGGCCCTAAACTGAC
ACAATGTTTTTGATCTCTTTAACCTCATCTACCTCAGGCAACAATGTTTT
TGATCTCTTTAACCTCATCTACCTCAGGCAGTGCTCATGGTGATTTGTG
CTCATGGTGATTT
>RefIdentifier2
CATCTACCTCAGGCAACCTCATGGTATTTGTGCTCATGGTGATTCCCTA
TCTACTTTTGAACAATGTTTTTGATCTCTTTAACCTTCTCTTTAACCTCCT
CAGGCAGTGGATGATGACTGACTGACTGTTTGATCGTGACTGATCGTG
ATCTTTTTTACGGGACATTAAAAGGCGGGCCCTAAACTGAC
./bwa aln indexfile readfile.fastq > BWAout.sai
./bwa samse indexfile BWAout.sai readfile.fastq > BWAout.sam
@SQ SN:RefIdentifier1 LN:124
@SQ SN:RefIdentifier2 LN:133
@SQ SN:RefIdentifier3 LN:189
@SQ SN:RefIdentifier4 LN:140
@SQ SN:RefIdentifier5 LN:120
@SQ SN:RefIdentifier2 LN:133
@SQ SN:RefIdentifier3 LN:189
@SQ SN:RefIdentifier4 LN:140
@SQ SN:RefIdentifier5 LN:120
Any help is much appreciated, thanks in advance.
Regards
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