splicing junctions collection

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splicing junctions collection

Postby ABQ » Wed Jan 25, 2012 6:47 pm

There is a statement associated with Splice junction collection (FBrf0212682) that reads:
The file "Cleanup_Junctions_w_counts.txt.bz2" contains a list of 67,317 junctions from the Illumina RNA-Seq data that we analyzed in Graveley et al.; this is the Illumina-only dataset.

How possibly can I download such a file? It doesn't seem to be listed on Flybase's ftp downloads...
Posts: 4
Joined: Wed Jan 25, 2012 4:49 pm

Re: splicing junctions collection

Postby gil519 » Thu Jan 26, 2012 11:29 am


Sorry about the oversight. Thanks for pointing it out. The file is now up on the FlyBase ftp site:
ftp://flybase.net/flybase/associated_fi ... counts.txt

The publication report for FBrf0212682 will also be updated to have a link to this file (as of FlyBase release 2012_02).


P.S. The first four columns in the file are Junction_ID (format: chr_start_stop), chromosome, start, stop, followed by a read count and entropy score column for each sample. The samples are labeled in the table using BS numbers which have the following translations (note that the columns are not necessarily presented in this order):
BS40 embryos0-2hr
BS43 embryos2-4hr
BS46 embryos4-6hr
BS49 embryos6-8hr
BS54 embryos8-10hr
BS55 embryos10-12hr
BS58 embryos12-14hr
BS62 embryos14-16hr
BS66 embryos16-18hr
BS67 embryos18-20hr
BS71 embryos20-22hr
BS73 embryos22-24hr
BS107 L1larvae
BS111 L2larvae
BS113 L3larvae_12hr_post_molt
BS196 L3larvaePS_1-2
BS200 L3larvaePS_3-6
BS203 L3larvaePS_7-9
BS129 white_prepupae
BS133 WPP_12hr
BS136 WPP_24hr
BS137 pupae_WPP_2d
BS140 pupae_WPP_3d
BS143 pupae_WPP_4d
BS150 adult_male_1d
BS156 adult_male_5d
BS162 adult_male_30d
BS153 adult_female_1d
BS159 adult_female_5d
BS165 adult_female_30d
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Joined: Thu Jan 26, 2012 10:47 am

Re: splicing junctions collection

Postby ABQ » Thu Jan 26, 2012 3:39 pm

Thank you a lot for this prompt reply and the update. Flybase rules!
Posts: 4
Joined: Wed Jan 25, 2012 4:49 pm

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