Question: How To Add Alignment To The Maf
gravatar for chengyuyan
6.5 years ago by
chengyuyan10 wrote:
Hi galaxy, I'm trying to know the coding potential of my RNA-seq transcripts by phylogeny analysis. So I want to generate a FASTA file that includes ORF of my sequence and 29 other mammalian species. I used"Extract MAF blocks" and "Stitch MAF blocks" using my RNA-seq data(gtf file from cuffcompare) as intervals. But the final FASTA file doesn't include my sequence. How can I add my sequence to the final FASTA so that it includes both the 29 mammalian genome and my sequence? Thanks in advance.Lyni.
galaxy • 1.6k views
ADD COMMENTlink modified 6.4 years ago by Jennifer Hillman Jackson25k • written 6.5 years ago by chengyuyan10
gravatar for Jennifer Hillman Jackson
6.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Lyni, Are you still having problems with your analysis? If so, then I can point you to a few tools that can help. - "FASTA manipulation" -> "Tabular-to-FASTA" and "FASTA-to-Tabular" - "Text Manipulation" -> "Concatenate datasets" - "Filter and Sort" -> "Sort" I am not sure how many RNA-seq transcripts you have, if just one, then concatenate that fasta sequence with the others into a single fasta file. If you have several, then they are likely named already (by the Extract MAF process) so that they can be grouped together by sorting. Convert the fasta data to tabular, concatenate, sort, then convert back to fasta. Thanks for using Galaxy, Jen Galaxy team
ADD COMMENTlink written 6.4 years ago by Jennifer Hillman Jackson25k
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