CCLE read bed file

Q&A
1

From a post I saw on here, all samples’ raw sequencing data are not available due to privacy constraints.
I would like to compare between the expression of this data set and other publicly available data sets (descartes, and others) and they use different annotation files for gene identification.

Do you have available just bed files of aligned reads so that I can map reads to genes myself?

For example files with the following columns:
chrom, read_start, read_end

BTW, thanks so much for the work/continued attention at this forum. Much appreciated.

2

Hi, thanks for your message. By ‘bedfile of aligned reads’ do you mean the gtf file for our rnaseq? Or are you looking for CNV/mutations annotation files? As of now we haven’t unified these across our pipelines yet. But it is in our todo list of activities.

For rnaseq you can find more information on this here.

3

I mean for example a file like this (from road map):

CHROM START END READ_ID STRAND
chr1 135007 135068 HS9_79:4:1101:20122:7348.L -
chr1 136892 136950 HS9_79:4:1101:20557:26147.R +
chr1 137972 138024 HS9_79:4:1101:3356:38389.L -
chr1 629280 629355 HS9_79:4:1101:14711:32517.L -
chr1 634513 634562 HS9_79:4:1101:2860:3464.L -
chr1 634518 634593 HS9_79:4:1101:8193:7522.L -
chr1 634505 634550 HS9_79:4:1101:20879:8166.L -
chr1 634504 634549 HS9_79:4:1101:5670:9135.L -
chr1 634506 634580 HS9_79:4:1101:14304:12224.R +
chr1 634510 634585 HS9_79:4:1101:18775:15869.L -

Each line represents one RNA seq read from one sample

4

Ah, I see. Unfortunately we don’t have that data available.

5

Ok, Thanks for the update!