User: chatterjee.arumoy

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Posts by chatterjee.arumoy

<prev • 9 results • page 1 of 1 • next >
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GO Gene Set Enrichment Analysis for maSigPro output
... 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 ...
masigpro clusterprofiler written 7 weeks ago by chatterjee.arumoy20
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ComBat-seq adjustment of batch effects
... 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 ...
sva batch effects rna-seq combat-seq edger written 9 weeks ago by chatterjee.arumoy20
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Batch effect correction in RNA-seq analysis by maSigPro
... 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 ...
time-series masigpro rna-seq written 9 weeks ago by chatterjee.arumoy20
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Comment: C: GTF/GFF file for feature count
... Thanks a lot, Devon. I really appreciate your help. ...
written 11 weeks ago by chatterjee.arumoy20
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Comment: C: Need to convert gene IDs for GAGE pathway analysis
... 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.arumoy20
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Comment: C: ERROR: failed to find the gene identifier attribute in the 9th column of the pro
... 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.arumoy20
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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.arumoy20
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Comment: C: ERROR: failed to find the gene identifier attribute in the 9th column of the pro
... 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.arumoy20 • updated 4 months ago by GenoMax94k
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ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
... 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 ...
featurecounts written 9 months ago by chatterjee.arumoy20 • updated 4 months ago by GenoMax94k

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