Problem mapping SOLiD reads with Bowtie1

Question

[biostart]

Hello,

Could you please have a look, what goes wrong?

I can not map old third-party SOLiD reads using Bowtie1 (it does not recognize SOLiD reads), please help! I am running Bowtie (Bowtie1) with the following command:

bowtie -t -v 2 -p 8 -m 1 -c -C hg19-Color filename.fastq filename.map

The hg19-Color is the colorspace index created using bowtie-build -C hg19.fa hg19-Color.

The .fastq file used as input was obtained by converting the corresponding .sra file downloaded from the SRA Archive using fastq-dump filename.sra.

The fastq file looks like this:

@SRR490054.1 head0094_20100208_1_EL19_K562_1pM_2_11_81_F3 length=35
T3.2230220232.1210..2201....123..222
+SRR490054.1 head0094_20100208_1_EL19_K562_1pM_2_11_81_F3 length=35
!&!%%&.65%%/;!%(1%!!)-.*!!!!*>'!!):%
@SRR490054.2 head0094_20100208_1_EL19_K562_1pM_2_11_360_F3 length=35
T0.2211222022.2321..2211....121..132
+SRR490054.2 head0094_20100208_1_EL19_K562_1pM_2_11_360_F3 length=35
!%!)(%+&(%%%&!(%&%!!&-%)!!!!&*%!!&'%
@SRR490054.3 head0094_20100208_1_EL19_K562_1pM_2_11_385_F3 length=35
T0.2233121323.2322..2011....222..223
+SRR490054.3 head0094_20100208_1_EL19_K562_1pM_2_11_385_F3 length=35
!5!%%%/=%%)'<!%.7%!!&*0)!!!!'*)!!))(

After running Bowtie, I get the following output:

Time loading forward index: 00:00:04
Time loading mirror index: 00:00:04
Time loading reference: 00:00:02
End-to-end 2/3-mismatch full-index search: 00:00:00
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 1 (100.00%)
No alignments

Do you think there is something wrong with the input fastq file, or the Bowtie parameters?

Answer 1

[jotan]

bowtie -t -v 2 -p 8 -m 1 -c -C hg19-Color filename.fastq filename.map

I think it could be the smallcaps -c in the bowtie command.

According to the manual:

-c The query sequences are given on command line. i.e. <m1>, <m2> and <singles> are comma-separated lists of reads rather than lists of read files.

Bowtie would be expecting a list of reads on the command line. That's why:

# reads processed: 1

[biostart]

Thank you, I removed the "-c", and it seems to work now.