Question: Fetch Alignments using Stitch Gene blocks, but '-' strand has been joined wrong
gravatar for yanghaobentley
3.0 years ago by
yanghaobentley0 wrote:

      As I use Fetch Alignments => Stitch Gene blocks extract genes from the maf file according to the BED coordination(The BED file contains the CDS position, start codon position, stop codon position, and I want to extract a complete gene with joined exons), I've found this problem: if the gene is in the '+' strand in the BED file, there is no problem at all. But if it is in the '-' strand, as each gene in the BED file has been separated into different exons (written in CDS in the file), its join will be a bit weird. As I check the sequence that the start codon goes to the end, and the stop codon goes to the front, and I guess the exons in between will be joined in a reverse order.
        How can I solve this? Do I have to change my coordination in the BED file?

stitch gene blocks • 726 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by yanghaobentley0

Hello, We are examining the shared history and will get back to you shortly. Thanks, Jen, Galaxy team

ADD REPLYlink written 3.0 years ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I just sent the details for the result directly by email. 

In short, the extracted sequences are a match for the MAF blocks, both in content and orientation. Sequences from this tool suite are reported in the direction of transcription with respect to the base genome of the input BED/Interval transcript dataset (dm6 in this case).

BED (and Interval) datasets always have coordinates reported in the forward direction with strand used as a modifier for the orientation of the region (can be interpreted as the direction of transcription for BED datasets representing transcripts or portions of transcripts). MAF datasets also have coordinates reported in the forward direction for the base genome, with strand in this file format used as a modifier for the other aligned genome(s) orientation.

Thanks! Jen, Galaxy team


ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k
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