Update README.md - Githubissues

lgmgeo commented 2 years ago

Dear Jayne,

Please find additional information for the README.md file.

I hope you will find them useful.

Best regards,

Véronique

lgmgeo commented 2 years ago

Here are the count differences for each type of MEI between:

the Mobster distribution (2018)
the current update I just did (2022) <html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

| hg19_alul1svaerv.rpmsk | alu_l1_herv_sva_other_grch38_accession_ucsc.rpmsk | 20220530_alu_l1_herv_sva_GRCh37_ucsc.rpmsk | 20220530_alu_l1_herv_sva_GRCh38_ucsc.rpmsk -- | -- | -- | -- | -- SVA | 3733 | 5750 | 4027 | 5913 Alu | 1194734 | 1238897 | 1244709 | 1269382 L1 | 951780 | 1001410 | 987052 | 1022089 HERV | 21361 | 21240 | 22128 | 21939 | | | | Total | 2171608 | 2267297 | 2257916 | 2319323

It is to notice that:

only the HERV (human ERV) was distributed in your GRCh38 version (alu_l1_herv_sva_other_grch38_accession_ucsc.rpmsk)
while all ERV (even not human) was distributed in your GRCh37 version (hg19_alul1svaerv.rpmsk)

I decided to keep only the HERV in the 2 updated files (20220530_alu_l1_herv_sva_GRCh3*_ucsc.rpmsk).

lgmgeo commented 2 years ago

The 2 updated files (20220530_alu_l1_herv_sva_GRCh3*_ucsc.rpmsk) are available at: https://www.lbgi.fr/~geoffroy/Partage/Jayne/

jyhehir commented 2 years ago

contents of the pull request look fine. But please update it to point to the development branch so it will be included in an release, I would also prefer the files to be included as an update to the resources directory.

Thanks for your input!

lgmgeo commented 2 years ago

No problem to update my pull request to point to the development branch. But which one?
The 2 updated files are too big to be included as an update to the resources directory. That's why I put them available on a ftp site : https://www.lbgi.fr/~geoffroy/Partage/Jayne/

jyhehir commented 2 years ago

sorry for the confusion I meant the branch "develop".

jyhehir / mobster

Update README.md #51