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