using BWA to align SOLiD fastq files from 1000 Genomes

[tgenahmet]

Hi All,

I've been playing with BWA to align some color space data from 1000 Genomes. So far all my alignments are TNNNNNNNNNNNNNNNN's.

I'm trying to figure out the correct procedure for using BWA with (color spaced) fastq files.

In this thread lh3 says:

Alignment is done in color space. After alignment, color reads are translated to nucleotides essentially with the code in maq's csmap2nt.

But in this thread it sounds like the input needs to be converted to nucleotide space.

bwa uses fastQ files with colors represented as ACGT, perhaps the 1000 genomes fastq files represents it as 0123? Also, bwa does not use the first color so you may have to strip it or use the solid2fastq script.

Here is what my input looks like (straight from 1000 Genomes FTP):

==> SRR008434_2.fastq <==
@VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_54
T3232322122230111000000220
+
!*(/&$'0++%/##3'%#(#&$%)#(
@VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_60
T0233233322023332023032223
+
!$##((#%$#%$,$#('$'#.#,+%#
@VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_93
T0102012101023023220003000

My output in sam format:

VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_54 77 * 0 0 * * 0 0 GNNNNNNNNNNNNNNNNNNNNNNNNN !##$&&&$)#.*(#%#.%$&'*%#$#
VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_54 141 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNN !*(/&$'0++%/##3'%#(#&$%)#(
VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_60 77 * 0 0 * * 0 0 GNNNNNNNNNNNNNNNNNNNNNNNNN !&%%%%&5)#,'%#$&)$%'$&,%(%
VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_60 141 * 0 0 * * 0 0 TNNNNNNNNNNNNNNNNNNNNNNNNN !$##((#%$#%$,$#('$'#.#,+%#
VAB_SOLiD0097_20080822_2_Pilot_1_Ceph_11994_A_Lib_1_2Kb_MP1561_6_93 77 * 0 0 * * 0 0 GNNNNNNNNNNNNNNNNNNNNNNNNN !&8';#'$.'&(?>:&',+6<<,56&

I indexed the reference genome using "bwa index -c", aligned using "bwa aln -c", then a "bwa sampe". No errors were reported in any of the steps.

Any ideas?

[pliang]

I had to agree with what chipper said that "bwa uses fastQ files with colors represented as ACGT". I had to give it up using the color space sequence directly. Instead of doing your own alignment, you may try use the alignment data they provided. Sorry I couldn't be more helpful.