Question: use bowtie for illumina with phred33?
gravatar for valdirbarth
22 months ago by
valdirbarth60 wrote:

Hi, I am a newbie on this field. I am using tools, and bowtie for aligning sequences and for some reason the default that it uses is phred64 instead of phred33 (like the latest downloadable version of bowtie). The illumina seq files I get are phred33 and work perfectly in my local bowtie.

I know I can use FastQ Groomer to make my fastq files phred64, but it takes forever. I was wondering if there is a way to use bowtie (version 1) with the phred33 parameter in

rna-seq alignment bowtie • 598 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by valdirbarth60
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The current version "Bowtie for Illumnia" in the Tool Shed (and installed at accepts fastqsanger sequence as input (Fastq sanger with Phred +33 quality score scaling). The tool produces output appropriate for use with other tools at the public Main website only when fastqsanger data is used. Datasets must be assigned the datatype fastqsanger for most tools to even recognize them as proper input.

This is how to prep your files. It includes instructions about how to check the fastq type and make adjustments. If after running FastQC and the data is in fastqsanger format, or you know it is already, there is no need to run Fastq Groomer. Instead, just assign the datatype directly.

If running the prep steps, make this initial FastQC job run quicker by executing it against just a subset of the fastq dataset (Text Manipulation > Select first lines from a dataset with the line number to keep as a multiple of 4). The first few sequences (100 or so) is enough input to detect quality score scaling type. Running FastQC on all of the data can be done after to assess and act on the quality metrics reported (run on the full original dataset if not modified, or on the full Fastq Groomer output if it was used to make changes).

That said, the other tool option is Bowtie2. This is a better choice for most for many reasons. That tool also accepts/expects fastqsanger formatted input fastq data.

The Fastq Groomer can convert between fastqsanger and fastqillumina (or any of the others, either way), but converting from illumina > sanger is not useful for most.

If you still need help after doing the above, please let us know.

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink modified 22 months ago • written 22 months ago by Jennifer Hillman Jackson25k
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