User: chatterjee.arumoy
chatterjee.arumoy • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 1 month, 1 week ago
- Joined:
- 11 months ago
- Email:
- c****************@gmail.com
Posts by chatterjee.arumoy
<prev
• 9 results •
page 1 of 1 •
next >
0
votes
0
answers
120
views
0
answers
... It might sound naive, but is there a way to do GO Gene Set Enrichment Analysis with DEGs obtained from maSigPro using clusterPRofiler? I am not sure how to sort the DEGs I obtained from maSigPro in decreasing order to provide to the gseGO function. Generally one do the sorting of DEGs with logFC if ...
written 7 weeks ago by
chatterjee.arumoy • 20
1
vote
0
answers
237
views
0
answers
... Hi,
If I have done my RNA seq with 4 samples X 3 replicates each in two batches (see below for the design matrix):
1) Is it correct to adjust batch effects on the raw count file first by ComBat-seq (Zhang et.al., 2020) and then process the output by edgeR?
CONDITIONS SAMPLES BATCH
T1 ...
written 9 weeks ago by
chatterjee.arumoy • 20
0
votes
0
answers
156
views
0
answers
... Hi,
I am using maSigPro to do a single series time course RNA-seq analysis. My design matrix looks like as follow:
> design
Time Replicates Group Batch
Array1 0 1 1 A
Array2 0 2 1 A
Array3 0 3 ...
written 9 weeks ago by
chatterjee.arumoy • 20
0
votes
1
answer
5.4k
views
1
answers
Comment:
C: GTF/GFF file for feature count
... Thanks a lot, Devon.
I really appreciate your help. ...
written 11 weeks ago by
chatterjee.arumoy • 20
0
votes
2
answers
1.9k
views
2
answers
... Hi Andrea Wall,
I am facing the same problem as yours regarding converting gene names to Entrez gene IDs.
If you had found the solution, would you please share it here?
Thanks in advance,
Arumoy.
...
written 11 weeks ago by
chatterjee.arumoy • 20
0
votes
1
answer
1.4k
views
1
answers
... Thanks, Chris S.
It seemed to work for me.
Since I am not well versed with grep, please kindly tell me (us) how did you fix the GTF file? And where from could we learn more about handling this type of issues.
Thanks a lot. ...
written 3 months ago by
chatterjee.arumoy • 20
0
votes
1
answer
5.4k
views
1
answers
Comment:
C: GTF/GFF file for feature count
... Hi, I have a similar problem with my GTF file. Feature count is giving the error "failed to find the gene identifier attribute in the 9th column of the provided GTF file." Please kindly if you tell me how to remove the " and wide space.
Arumoy. ...
written 3 months ago by
chatterjee.arumoy • 20
0
votes
1
answer
1.4k
views
1
answers
... I see the "gene_id" is present. I also converted the .gtf file into an excel table also and the 9th column is indeed "gene_id". Each column of the .gtf file has 335791 entries.
#gtf-version 2.2
#!genome-build Amel_HAv3.1
#!genome-build-accession NCBI_Assembly:GCF_003254395.2
#!annot ...
written 9 months ago by
chatterjee.arumoy • 20
• updated
4 months ago by
GenoMax ♦ 94k
2
votes
1
answer
1.4k
views
6 follow
1
answer
... Hi,
I am trying to use featureCounts to analyse my RNA-seq data with Apis mellifera.
My Code and error are as follows. r
/softwares/subread-2.0.0-source/bin/featureCounts
-T 16
-p
-s 1
-a /home/axel/arumoyc/alignment/GCF_003254395.2_Amel_HAv3.1_genomic.gtf
-t exon
...
written 9 months ago by
chatterjee.arumoy • 20
• updated
4 months ago by
GenoMax ♦ 94k
Latest awards to chatterjee.arumoy
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1417 users visited in the last hour