Question: Download Bowtie2 alignment
gravatar for a.chembath1
6 months ago by
a.chembath10 wrote:


I have done a saturation mutagenesis experiment and sequenced the resulting PCR products via Illumina NGS. I now have a large NGS dataset. I have used Bowtie2 to get an alignment which has worked very well. Now I need to download the alignment, first to trim off the end sequences of various lengths (Bioedit?) and then secondly analyse the saturated codons (Excel). Can anyone please tell me how to convert the BAM/SAM Bowtie2 file into one readable by Bioedit and/or Excel?

Thank you.

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by a.chembath10
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The SAM datatype is a version of tabular formatted data.

Or, you can convert SAM/BAM data to an interval datatype with the tool NGS: SAMtools: Convert SAM to interval. Interval is also a more specific version of tabular data.

Datatype FAQ:

Excel will accept any tabular data as an input (with limits on the number of lines). I'm not sure about Bioedit -- I haven't used it and the expected input formats are not clearly stated on the tool's website. You'll need to review the tool documentation/support to find out what data it works with.

There are many other tools to manipulate data within Galaxy if you need to rearrange before downloading. Start with those under the group Text manipulation. Or, you can download it first, then manipulate the data locally line command.

If you need a SAM dataset without a header, you can remove that with a command-line text editor once downloaded (most SAM datasets will probably be too large for Excel use directly), or if you have the BAM version, use NGS: SAMtools: BAM-to-SAM and output excluding the header, then download.

Galaxy tutorials: Support FAQs:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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