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add link to gistic file formats #456
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January 18, 2020 14:46
add sample inclusion information
jharenza
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Linking to the GenePattern is not adequate in my opinion. I am glad you specifically highlight sample_seg_counts.txt because I don't see any reference to that filename in the documentation page linked here.
The documentation page you linked to includes the following:
Other result files include:
regions_track.conf_XX.bed broad_significance_results.txt (only output if run.broad.analysis is set to "yes") broad_values_by_arm.txt (only output if run.broad.analysis is set to "yes") freqarms_vs_ngenes.pdf (only output if run.broad.analysis is set to "yes") arraylistfile.txt (only output if an array.list.file is provided as input) all_data_by_genes.txt broad_data_by_genes.txt focal_data_by_genes.txt sample_cutoffs.txt amp_qplot.v2.pdf and amp_qplot.v2.ps (do not contain gene labels) del_qplot.v2.pdf and del_qplot.v2.ps (do not contain gene labels)
There are at least two modules that use the broad_values_by_arm.txt file that's not described in the documentation.
Consider what files people need to complete the descriptive analyses of these data and a bit about how they would use them. For example, what files would be necessary to identify recurrently altered genes? More context is better and is likely to reduce friction for analysts.
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thanks, will update |
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Subsumed by #507 |
jaclyn-taroni
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Feb 7, 2020
* add v14 release docs -update `release-notes.md` -update `data-files-description.md` -update `data-formats.md` * Update download-data.sh add new folder for V14 to download scipt * remove intersect_cds_WXS.bed per @cansavvy [comment](#432 (comment)) * add intersect_cds_lancet.bed and description from @cansavvy [comments](#507 (comment)) * Update release-notes.md - add removal of polyA+stranded samples that were still in file in v13 * Update data-formats.md add more information on gistic output files, to replace PR [#456](#456) * Reorganize derived CN section and make formatting consistent * Add links to relevant subtyping modules * Update release-notes.md readme update for upcoming lancet MAF per issue [here](#512) * Update doc/release-notes.md yup, nice catch Co-Authored-By: Jaclyn Taroni <jaclyn.n.taroni@gmail.com> * Update release-notes.md fix embryonal broad histology Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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Purpose/implementation Section
What scientific question is your analysis addressing?
GISTIC analysis
What was your approach?
Adding link to information about GISTIC file formats contained in the
pbta-cnv-cnvkit-gistic.zipfile.What GitHub issue does your pull request address?
#417
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Sorry this ticket escaped me, but does a link to the website suffice here?
Is there anything that you want to discuss further?
No
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes
Results
What types of results are included (e.g., table, figure)?
NA
What is your summary of the results?
NA