Where Can I Download Some Bam Files?
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10.5 years ago
snakesgun ▴ 150

Hi, all Recently, I have build a web based RNA-Seq analysis platform and It has run successfully. However, I have no bam file of transcriptome to test my platform. Where can I find some bam files which have been released? Thanks~~!!

bam rna-seq bioinformatics • 38k views
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How about finding BAM files representing viral genomes, such as HIV? None of these sites mentioned has high coverage represented. Any ideas? Thank you

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8.1 years ago

If you want smaller BAM files for testing, here is a ENCODE collection that starts at around 40 MB:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq

Here is an example (to show it, you can paste the link as it is into the "Custom track" text box in the UCSC genome browser):

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqGm12878G1bAlnRep1.bam

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10.5 years ago
Geparada ★ 1.5k

Here you have FASTQ and BAM files from different human cell lines organized in a pretty nice interface:

http://genome.crg.es/~jlagarde/encode_RNA_dashboard/

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Nice, hadn't seen that!

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The links in this interface seem to refer to dead UCSC links now unfortunately (presumably due to referring to hgdownload-test URL). Cool resource though!

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10.5 years ago

There are of course many many places to look, but one place to start is the ENCODE RNA-seq data hosted at UCSC, e.g.:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeSydhRnaSeq/

and the other RNA-seq tracks at http://genome.ucsc.edu/ENCODE/downloads.html.

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10.5 years ago
Paolo ▴ 320

1000 genomes project gives access to all collected data: http://www.1000genomes.org/data

Quick links:

The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via our mirrored ftp sites.

EBI FTP: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/

NCBI FTP: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/

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4.1 years ago

For a quick-gratification one-liner (instead of multi-step and multi-MB approaches), one could just use that command (after installing samtools):

samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17:7512445-7513455 -O bam > test.bam

I'll leave the data gathered from it to your discretion though, not sure of which regions from 1000 genomes would work best for your usecase, 17:7512445-7513455 might not be what you are looking after, but you get the idea.

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10.5 years ago

You can also use the cool Data Slicer app to retrieve subset of data from 1000 genomes BAM files. Command-line utility documentation here and web-app here. Using Data Slicer you can import BAM files on-the fly to your web app.

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do you maintain this separately from https://github.com/roryk/tiny-test-data ?

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