# CCLE read bed file

**URL:** <https://forum.depmap.org/t/ccle-read-bed-file/577>\
**Category:** Q&A\
**Tags:** data\
**Created:** [April 25, 2021, 10:36am UTC](https://forum.depmap.org/t/ccle-read-bed-file/577 "2021-04-25T10:36:17Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![yonnierosensk](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yonnierosensk/32/213_2.png) [@yonnierosensk](https://forum.depmap.org/u/yonnierosensk)\
**Post date:** [April 25, 2021, 10:36am UTC](https://forum.depmap.org/t/ccle-read-bed-file/577/1 "2021-04-25T10:36:17Z")

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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.

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [April 26, 2021, 4:43pm UTC](https://forum.depmap.org/t/ccle-read-bed-file/577/2 "2021-04-26T16:43:37Z")

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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](https://forum.depmap.org/t/missing-genes-in-topmed-gencode30-gtf-file/71).

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<div class="post-metadata">

**Author:** ![yonnierosensk](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yonnierosensk/32/213_2.png) [@yonnierosensk](https://forum.depmap.org/u/yonnierosensk)\
**Post date:** [April 26, 2021, 6:57pm UTC](https://forum.depmap.org/t/ccle-read-bed-file/577/3 "2021-04-26T18:57:46Z")

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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

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<div class="post-metadata">

**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [April 26, 2021, 8:00pm UTC](https://forum.depmap.org/t/ccle-read-bed-file/577/4 "2021-04-26T20:00:12Z")

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

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<div class="post-metadata">

**Author:** ![yonnierosensk](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/yonnierosensk/32/213_2.png) [@yonnierosensk](https://forum.depmap.org/u/yonnierosensk)\
**Post date:** [April 27, 2021, 3:30pm UTC](https://forum.depmap.org/t/ccle-read-bed-file/577/5 "2021-04-27T15:30:47Z")

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Ok, Thanks for the update!