Question: Need help with "Stitch MAF blocks" tool
gravatar for athonysmith
4.3 years ago by
athonysmith10 wrote:

The "stitch-maf-blocks" report that I get 763,251 sequences. After I download the result, the number of the sequences is actually 988,610 sequences. This number is equal to the every segments in the exon not the number of lines of bed file.

I have used this tools for several times. This situation is not found before. Every time, the number of found sequences reported is equal to the number of bed file' lines,which may contain several exons for a line.



Tool name: Stitch MAF blocks
Tool version: 1.0.1
Tool ID: Interval_Maf_Merged_Fasta2


ADD COMMENTlink modified 4.3 years ago by Jennifer Hillman Jackson25k • written 4.3 years ago by athonysmith10
gravatar for Jennifer Hillman Jackson
4.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If you need exact counts (the ones included in datasets are sometimes estimates), then a tool like "Text Manipulation -> Line/Word/Character count of a dataset" would be a good choice. 

If you would like to share a link to the history with the datafile, we can also take a look to rule out a problem. Email the share link to along with a link to this post (to help with cross-referencing the two).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.3 years ago by Jennifer Hillman Jackson25k

When input .GTF, 'Stich MAF blocks'(SMB) will report 'exon' as block. When input .bed, SMB will report 'transcript' as block. I wrongly mix them up. @Jen, many thanks!

ADD REPLYlink written 4.3 years ago by athonysmith10

I think it may be a bug in 'sticth MAF blocks'. I guess it could be the large number of blocks which cause the stitching step does not happen. What we get is the extracted segments un-stitched. In my dataset history, the 56th step using the dataset of 54th step. When I reduce the stitching block number, as in 58th step on 57th dataset, it becomes normal. I'll split the dataset into several parts in the future, to avoid chocking the server.

Some information history link: related history id: 54,56 discussion link: A: Need help with "Stitch MAF blocks" tool


ADD REPLYlink written 4.3 years ago by athonysmith10
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