Closed johnsolk closed 5 years ago
Hi @ljcohen, can you paste in the quant_DE.yml
file for this please? We need to either provide the gene_trans_map or set the deseq2 gene_trans_map
parameter to false
. https://dib-lab.github.io/eelpond/diffexp, https://dib-lab.github.io/eelpond/deseq2
Setting gene_trans_map=false
solved this problem. Here is the .yml created with ./run_eelpond quant_DE.yml quantify
(which then crashed because of #89)
#################### Eelpond Pipeline Configfile ####################
basename: lab7
experiment: DE
samples: samples.tsv
#################### diffexp ####################
deseq2:
contrasts:
time0-vs-time6:
- time0
- time6
gene_trans_map: false
pca:
labels:
- condition
get_data:
download_data: false
use_ftp: false
salmon:
index_params:
extra: ''
input_trimmomatic_trimmed: true
quant_params:
extra: ''
libtype: A
trimmomatic:
adapter_file:
pe_path: ep_utils/TruSeq3-PE-2.fa
se_path: ep_utils/TruSeq3-SE.fa
extra: ''
trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25
assemblyinput:
assembly: '../data/nema_trinity.fasta'
assembly_extension: '_input'
fyi @ljcohen, the alternative would be to have this in the yaml
:
assemblyinput:
assembly: '../data/nema_trinity.fasta'
gene_trans_map: '../data/nema_trinity.fasta.gene_trans_map'
assembly_extension: '_input'
eelpond
just needs to know where to find the gene_trans_map
, if using it