Question: Help with downloading files from EBI SRA
1
gravatar for bwb012
3.5 years ago by
bwb01220
United States
bwb01220 wrote:

I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in order to observe differential gene expression. I have been messing around with Drosophila melanogaster experimental reads from the EBI SRA site. 

Most experiments are labeled as paired-end reads, however when I go to download the data there is usually only one file (some do have two). Does the one file mean that both ends are in the same file, and if so in what format? Aligned next to each other in one long read? Stacked on top of each other? Is there a way to check if reads are paired-end in one file? Or split paired-end reads that are all in one file into single-end reads?

Thank you in advance for any help with this issue.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by bwb01220
1

Hi, could you give examples (experiment accessions will be fine) of a couple of cases which are described as paired-end, but only have a single data file?

ADD REPLYlink written 3.5 years ago by Mark Crowe100

These are the two specific files I have been working with:

DRX013093: 454 GS Junior paired end sequencing; Transcriptome analysis of uninfected 3rd instar larvae of D. melanogaster.

DRX013094: 454 GS Junior paired end sequencing; Transcriptome analysis of Penicillium-fungus infected 3rd instar larvae of D. melanogaster.

 

But here are two more examples of files I have looked at that specifically say paired end in the title and yet only have one file:

DRX000774

: Illumina Genome Analyzer IIx paired end sequencing; SRig10098

ERX006127: AB SOLiD System 3.0 paired end sequencing; RNAi of signal transduction components in Drosophila S2 cells

ADD REPLYlink written 3.5 years ago by bwb01220
0
gravatar for Jennifer Hillman Jackson
3.5 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi - These runs are annotated as single. The available data files are slightly odd - no submitted (the original). Where did you see paired-end indicated in the methods? If not, then I would either assume single end or consider contacting the authors.

For reference: http://454.com/applications/transcriptome-sequencing/index.asp
Best, Jen, Galaxy team

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Jennifer Hillman Jackson23k
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