Question: Problems with the results of the tutorial Galaxy101: the first thing you should try
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gravatar for a_kathrin
20 months ago by
a_kathrin10
a_kathrin10 wrote:

I've run the workflow described in https://usegalaxy.org/u/aun1/p/galaxy101 and, by being careful particularly in the selection of the proper SNPs dataset (the one used in the tutorial), I've got completely different results, with the first 5 sorted exons having up to 1296 SNPs per exon (instead of 67 described in the tutorial). Even considering that the tutorial was designed in 2015 the difference is too deep to be explained by an update of the SNPs dataset. Any suggestion ?

thanks Kathrin

galaxy101 • 378 views
ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson24k • written 20 months ago by a_kathrin10
1

The newest version of this tutorial is available here: https://usegalaxy.org/galaxy101 (and has now a form of a wiki instead of Galaxy Page) so please follow that one.

I am unable to comment on the data difference, maybe someone else will.

ADD REPLYlink written 20 months ago by Martin Čech ♦♦ 4.3k
0
gravatar for a_kathrin
20 months ago by
a_kathrin10
a_kathrin10 wrote:

Hello, It has been very nice to receive the answer so soon, thanks a lot. By following the wiki page I've got results which are closer to the one of the tutorial but still deeply different, ie: less regions after joining exons and SNPs (6444 in my analysis vs 8016 in the tutorial), and finally the exon with the highest number of snps in my analysis is the number uc003bhh.4_cds_0_0_chr22_46256561_r with 30 snps (while the exon with 63 snps reported in the tutorial results is missing).

It seems somehow that the analysis is correct (the exon uc003bhh.4_cds_0_0_chr22_46256561_r has 30 snps also in the tutorials list of exons) but some exons have been neglected.

I'm new to Galaxy, so I wonder if this kind of waves in the data are simply due to the months elapsed between the 2015 version of Galay101 and the time of my analysis.

thanks a lot, k

ADD COMMENTlink written 20 months ago by a_kathrin10

There are two GENCODE releases available the UCSC Table browser: v22 and v23

v22 is used in the tutorial .. perhaps double check this data source?

ADD REPLYlink written 20 months ago by Jennifer Hillman Jackson24k
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