Question: Problem mapping SOLiD reads with Bowtie1
gravatar for biostart
4.4 years ago by
biostart350 wrote:


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

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%)
No alignments


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

sequencing chip-seq • 1.4k views
ADD COMMENTlink modified 4.4 years ago by jotan1.2k • written 4.4 years ago by biostart350
gravatar for jotan
4.4 years ago by
jotan1.2k wrote:

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


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"

ADD COMMENTlink written 4.4 years ago by jotan1.2k

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

ADD REPLYlink written 4.4 years ago by biostart350
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