Question: Question about downloading RNA-seq long reads and short reads for the same sample
0
gravatar for tunl
8 days ago by
tunl40
tunl40 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 • 188 views
ADD COMMENTlink modified 7 days ago by magdoll10 • written 8 days ago by tunl40
2

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

ADD REPLYlink written 8 days ago by Sej Modha1.8k

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 8 days ago by tunl40
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 8 days ago by genomax33k
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 8 days ago by Sej Modha1.8k

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

ADD REPLYlink modified 7 days ago • written 7 days ago by tunl40

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 7 days ago • written 7 days ago by tunl40
1
gravatar for magdoll
7 days 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 7 days ago by magdoll10

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

ADD REPLYlink written 7 days ago by tunl40

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

ADD REPLYlink modified 7 days ago • written 7 days ago by tunl40

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 7 days ago by tunl40
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