Hi all,
I've been having lots of trouble getting 36 million SOLiD reads aligned to hg18. I started using bwa, but less than 40% of my reads align, which seems pretty low. Posts on here suggesting there are bugs in the SOLiD module of BWA have made me look towards other solutions. The fastq file for the bwa input was created using the csfastaToFastq script.
Here's the bwa aln command Ive been using:
bwa aln -c hg18.cs.fa reads.part1.fastq
I've also tried bowtie, and can get over 54% of the reads to align, however when using samtools to import the resulting sam file I'm getting this:
[samopen] SAM header is present: 25 sequences.
Parse error at line 28: sequence and quality are inconsistent
Here's my bowtie command and the samtools import command:
bowtie_0.12.2/bowtie -t -C -S --nomaqround --best --snpfrac .001 -n 2 --chunkmbs 256 -e 90 -l 28 -p 6 hg18_c bfast_built_validation_reads_91.fastq bowtie_run1.sam
samtools import /home/jekeeble/storage/hg18/hg18.fa.fai ./bowtie_run1.sam bowtie_run1.bam
As you might guess, the fastq file used for the bowtie input was built using the bfast solid2fastq program.
Finally, i've also been trying to use BFast based on lh3's mention that many people are converging to that or bioscope for solid data. I can't seem to get beyond getting the bfast index built.
running:
bfast index -f hg18.fa -w 14 -n 5 -A 1 -m 1011..111 -i 2
produces this output:
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName hg18.fa.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: hg18.fa
space: [Color Space]
mask: 10111111011001100011111000111111
depth: 0
hashWidth: 14
indexNumber: 2
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: [Not Using]
numThreads: 5
tmpDir: ./
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from hg18.fa.cs.brg.
In total read 25 contigs for a total of 3080436051 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=25 and position=16571.
************************************************************
Currently on [contig,pos]:
[------10,---68000000]
[------25,------16571]
Sorting by thread...
bfast: RGIndex.c:743: RGIndexSort: Assertion `IsAPowerOfTwo(numThreads)==1' failed.
Aborted
Anyone have suggestions to where I should go from here? It's been a pretty frustrating day
. I"m also running shrimp, but it's taking its sweet time.
Thanks,
Jonathan K.
I've been having lots of trouble getting 36 million SOLiD reads aligned to hg18. I started using bwa, but less than 40% of my reads align, which seems pretty low. Posts on here suggesting there are bugs in the SOLiD module of BWA have made me look towards other solutions. The fastq file for the bwa input was created using the csfastaToFastq script.
Here's the bwa aln command Ive been using:
bwa aln -c hg18.cs.fa reads.part1.fastq
I've also tried bowtie, and can get over 54% of the reads to align, however when using samtools to import the resulting sam file I'm getting this:
[samopen] SAM header is present: 25 sequences.
Parse error at line 28: sequence and quality are inconsistent
Here's my bowtie command and the samtools import command:
bowtie_0.12.2/bowtie -t -C -S --nomaqround --best --snpfrac .001 -n 2 --chunkmbs 256 -e 90 -l 28 -p 6 hg18_c bfast_built_validation_reads_91.fastq bowtie_run1.sam
samtools import /home/jekeeble/storage/hg18/hg18.fa.fai ./bowtie_run1.sam bowtie_run1.bam
As you might guess, the fastq file used for the bowtie input was built using the bfast solid2fastq program.
Finally, i've also been trying to use BFast based on lh3's mention that many people are converging to that or bioscope for solid data. I can't seem to get beyond getting the bfast index built.
running:
bfast index -f hg18.fa -w 14 -n 5 -A 1 -m 1011..111 -i 2
produces this output:
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName hg18.fa.
Validating tmpDir path ./.
Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: hg18.fa
space: [Color Space]
mask: 10111111011001100011111000111111
depth: 0
hashWidth: 14
indexNumber: 2
repeatMasker: [Not Using]
startContig: 0
startPos: 0
endContig: 2147483647
endPos: 2147483647
exonsFileName: [Not Using]
numThreads: 5
tmpDir: ./
timing: [Not Using]
************************************************************
************************************************************
Reading in reference genome from hg18.fa.cs.brg.
In total read 25 contigs for a total of 3080436051 bases
************************************************************
Creating the index...
************************************************************
Warning: startContig was less than zero.
Defaulting to contig=1 and position=1.
************************************************************
************************************************************
Warning: endContig was greater than the number of contigs in the reference genome.
Defaulting to reference genome's end contig=25 and position=16571.
************************************************************
Currently on [contig,pos]:
[------10,---68000000]
[------25,------16571]
Sorting by thread...
bfast: RGIndex.c:743: RGIndexSort: Assertion `IsAPowerOfTwo(numThreads)==1' failed.
Aborted
Anyone have suggestions to where I should go from here? It's been a pretty frustrating day
![Smile](https://www.seqanswers.com/core/images/smilies/smile.png)
Thanks,
Jonathan K.
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