SOLiD reads unreadable to Bowtie after unpacking from .sra archive [still open]

Question

[biostart]

Hello,

I have downloaded a published MNase-seq dataset from the SRA archive, unpacked the .sra files, and obtained something like this:

@SRR430055.1 head0094_20100309_1_K562_2_16_40_F3 length=35
T322.2.232..222...3312.03333033333.3
+SRR490055.1 head0094_20100309_1_K562_2_16_40_F3 length=35
!+6-!&!/.5!!(/0!!!'%%+!&(1-,%%(+'%!/
@SRR430055.2 head0094_20100309_1_K562_2_16_106_F3 length=35
T321.2.320..220...3033.22300102021.3
+SRR430055.2 head0094_20100309_1_K562_2_16_106_F3 length=35
!78.!%!%%%!!,3)!!!%*&&!+5%'%)'2-,%!(
@SRR430055.3 head0094_20100309_1_K562_2_16_114_F3 length=35

Then I am trying to map this file with Bowtie, and it does not recognise it. I previously worked with Solexa, this is my first experience with SOLiD reads. Questions: 1) whether the reads above look normal, and if not, do you think there was a problem during unpacking from .sra? 2) If the reads look OK, what is a proper command line to run Bowtie with SOLiD reads? Thank you!

[User 59]

Bowtie or Bowtie2? Bowtie2 doesn't support colorspace AFAIK

[Tej Sowpati]

Also, AFAIK SOLiD output is normally a combination of two files, a .csfasta file with the read info, and a QV.qual file with quality info. The reads you posted are in colorspace FASTQ format, which I am not sure if bowtie supports (I could be wrong).

[Antonio R. Franco]

Bowtie1 is color space compatible. Bowtie2 does not

[Tej Sowpati]

Yes, but I meant the reads and quality information being in the same file. Whenever I used colorspace, I had separate files for reads and quality information.

[biostart]

Yes, I am using Bowtie1.

Could it be that I incorrectly unpacked the SRA file? I was using fastq-dump without additional parameters. Is the file listed above OK?

Aren't these symbols strange? !+6-!&!/.5!!(/0!!!'%%+!&(1-,%%(+'%!/

Answer 1

[igor]

Make sure you are adding the -C flag for colorspace reads in your Bowtie command.

[User 59]

You'll also need to build a colorspace index http://bowtie-bio.sourceforge.net/manual.shtml#colorspace-alignment

[biostart]

I added -C, but Bowtie still says:

Error: one or more quality files were specified with -Q but -f was not
enabled.  -Q works only in combination with -f and -C.

Answer 2

[Antonio R. Franco]

And consider that every dot is an unknown base with a very poor quality