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Question: Need help with "Stitch MAF blocks" tool
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gravatar for athonysmith
4.3 years ago by
athonysmith • 10
China
athonysmith • 10 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

 
bed stitch-maf-blocks gtf galaxy maf • 1.2k views
ADD COMMENT • link •
modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by athonysmith • 10
1
gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 galaxy-bugs@bx.psu.edu along with a link to this post (to help with cross-referencing the two).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
1

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 REPLY • link written 4.3 years ago by athonysmith • 10

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: https://usegalaxy.org/u/athony/h/t1 related history id: 54,56 discussion link: A: Need help with "Stitch MAF blocks" tool

Thanks!

ADD REPLY • link written 4.3 years ago by athonysmith • 10
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