Entering edit mode
4.7 years ago
cyntsc
•
0
I am trying to get 20 arabidopsis fasta files (transcripts) under specific criteria:
MRNA + infected leaves + fungi + <48 hpi + Illumina
The SRA-NCBI results are poor, the results in TAIR-DB are mainly related to annotations and other metadata, but they are not raw data like what I am requiring, and the ENA browser results are also poor according to the criteria I am looking for. There is another way to obtain these data sets that does not require mining within the publications.
Thanks, Cynthia
I believe you are mixing many things: a) the transcripts you are looking seems t be differentially expressed or highly expressed in a particular condition (fungi infection before 48hrs) b) SRA will store the raw data for such experiments, not the transcripts, then you will need to analyze that c) then, you will need to identify the experiment, collect the data and perform all the analysis steps (QC, align, quantify, DEG)
Hi again!
I am not trying to do DEG, what I am doing is concensus networks, so, what I require is the transcriptomes to quantify them and perform the whole stuff… So, where I am a little locked, it is regarding how how to get many of these fasta files at the same time (recommendation of tools or databeses, anything ) to avoid mining into the publications directly… Let me show you my query in the SRA:
In the repository of the SRA: View results as an expanded interactive table using the RunSelector. Send results to Run select
((((((((((("Arabidopsis thaliana"[Organism]) AND ("transcriptomic"[Source])) AND (("rna seq"[Strategy]) AND ("rt pcr"[Selection])) AND (("illumina"[Platform]) AND ("filetype fastq"[Properties]))))) AND (LEAF[Text Word] OR LEAVES[Text Word])))))) NOT "single"[Layout])
I got with this query 102 coincidences, but of these just 1 match the criteria :(… I hope to had explained better my requirement.
Thanks by advance.
Cynthia SC