Mark Ziemann

library("tictoc") library(XML) library(reutils) tic() eres

simpler ``` pysradb search --organism="Escherichia coli" --source="transcriptomic" --max=999000 > ecoli.tsv awk '{print $(NF-2)}' ecoli.tsv > ecoli_runs.tsv ```

Hi @apredeus , I noticed this also. It is an inconsistency between the Ensembl GTF and the cDNA file. For kallisto mapping, DEE2 uses the cDNA. `$ wget ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz` `$...

Thanks for investigating this Alex. In the next version of DEE we would like to include lincRNAs as well. So is it safe to concatenate the ncRNA.fa and cDNA.fa then...

First step - find the diff of the complete metadata and the one loaded on the webserver /mnt/md0/dee2/sradb$ comm -23

working on cgi newsearch.sh

This is the request email > Hello DEE2 user, > > SRA project SRP_ACCESSION have been added to the express queue for immediate processing. > For most SRA projects, this...

Need to manage errors more gracefully request.txt 100% 216 4.7KB/s 00:00 athaliana SRP218270 grep: SRP218293: No such file or directory grep: SRP218494: No such file or directory grep: SRP252639: No...

So the process is working from request to email, but there are some problems with the data provided For SRP216580 there are 17 runs in SRA but in the qc...

I will set you up with a devel environ similar tomorrow. For now are you able to ssh into prod and look around?