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
+SRR490054.1 head0094_20100208_1_EL19_K562_1pM_2_11_81_F3 length=35
@SRR490054.2 head0094_20100208_1_EL19_K562_1pM_2_11_360_F3 length=35
+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
+SRR490054.3 head0094_20100208_1_EL19_K562_1pM_2_11_385_F3 length=35
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%)
Do you think there is something wrong with the input fastq file, or the Bowtie parameters?