Question: Question about downloading RNA-seq long reads and short reads for the same sample
0
gravatar for tunl
5 months ago by
tunl50
tunl50 wrote:

We need to use RNA-seq long reads and short reads from the same sample to do some comparisons. I was wondering which websites may have both RNA-seq long reads (e.g. PacBio reads) and short reads for the same sample so we could download from there?

Any advice would be greatly appreciated.

Thank you very much in advance!

pacbio rna-seq long reads • 334 views
ADD COMMENTlink modified 5 months ago by magdoll10 • written 5 months ago by tunl50
2

You might want to look at Illumina hiseq and pacbio isoseq data on same set of samples- combined analysis help?

ADD REPLYlink written 5 months ago by Sej Modha2.6k

Thank you so much for your suggestion! I looked at this posting, but the paper they mentioned there does not provide their long reads and short reads datasets for downloading. This seems to be the situation in many papers: they do not provide their datasets of long reads and short reads. So I was wondering if there is any public website that collects some long reads and short reads datasets for the same samples so we could download from there? Thanks a lot!

ADD REPLYlink written 5 months ago by tunl50
1

The datasets for that paper are available: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1254204 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1254205

ADD REPLYlink written 5 months ago by GenoMax42k
1

I am not exactly sure what you are after but I found this paper https://www.nature.com/articles/s41467-017-00050-4 that mentions that some PacBio data is available online: http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/list.html

ADD REPLYlink written 5 months ago by Sej Modha2.6k

Thank you so much! This PacBio site looks great. I'll take a look.

ADD REPLYlink modified 5 months ago • written 5 months ago by tunl50

Thank you so much for providing me the GSM datasets links! I really appreciate it. I looked into these datasets, but this paper only gave us the processed data (aligned reads for Illumina; error-corrected reads for PacBio).

ADD REPLYlink modified 5 months ago • written 5 months ago by tunl50
1
gravatar for magdoll
5 months ago by
magdoll10
magdoll10 wrote:

The MCF-7 dataset as mentioned above does have a long read data and public short read data.

I've compiled a (very selective) list of PacBio long read RNA publications, some of them do have accompanying short read data: https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki/Iso-Seq-Publications

ADD COMMENTlink written 5 months ago by magdoll10

This is great. Thanks a lot! I’ll take a look at them.

ADD REPLYlink written 5 months ago by tunl50

[DELETED, sorry I initially replied at a wrong place]

ADD REPLYlink modified 5 months ago • written 5 months ago by tunl50

For the "previously published MCF-7 Illumina dataset" (http://www.genomebiology.com/2014/15/1/R15), I can't seem to find the Illumina dataset from this paper (it mentioned "Additional file 1", but "Additional file 1" is actually a .xls file (a Table).) Any ideas? Thanks so much!

ADD REPLYlink written 5 months ago by tunl50
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