User: krushnach80

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krushnach8090
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Posts by krushnach80

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Comment: C: featurecount command to extract read count from bam files
... yes Im using the output for deseq2 ...
written 4 days ago by krushnach8090
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featurecount command to extract read count from bam files
... I m using this featurecount command to extract read count from my bam files , is it the correct one im using or there is some issue with my command . featureCounts -T 40 -p -A -s -f -O -t exon -g gene_id -a /home/punit/ERCCgencode.v21.annotation.gtf -o /home/punit/FCOUNT/newhl60.txt ~/bamfiles ...
rna-seq written 4 days ago by krushnach8090 • updated 4 days ago by Devon Ryan65k
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Comment: C: Plot heatmap of differentially expressed genes identified by DESeq2 a R coding p
... I was looking for this thank your for the solution but i have one doubt why are you using this can you explain `& !is.na(res$padj),`? ...
written 8 days ago by krushnach8090
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Comment: C: Deseq2 differential result
... yes , I was wondering if I can filter result out instead of getting the final values where I would set threshold to filter result ...
written 10 days ago by krushnach8090
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Comment: C: Deseq2 differential result
... no not exactly , I was wondering can i get it done while running the pipeline ...
written 10 days ago by krushnach8090
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Comment: C: Deseq2 differential result
... yes I know but as I said i have like 18000 in my list and most of them wouldn't be of much use so how do I filter out the result .Is it based on some cutoff or what other parameters ? ...
written 10 days ago by krushnach8090
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Comment: C: Deseq2 differential result
... okay so i have to decide what threshold I m going to use that is what you mean? ...
written 10 days ago by krushnach8090
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Deseq2 differential result
... I m running Deseq2 pipeline my final result file is like 18,000 genes .So how do take the differential expressed genes from my list of genes .Do i sort if based on p value or is there a way to do inside the deseq2 before getting the final list of genes Any help or suggestion would be appreciated . ...
R rna-seq written 10 days ago by krushnach8090 • updated 10 days ago by Radek700
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Comment: C: What is the best way to match gene id with gene name.
... awk '{ for (i = 1; i <= NF; i++) { if ($i ~ /gene_id|gene_name/) { printf "%s ", $(i+1) } } print "" }' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 can anyone explain me this what ...
written 11 days ago by krushnach8090
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Comment: C: Xenopus tropicalis Ensembl Gene IDs and Transcripts ID with BiomaRt
... how can i use this "transAndGene" to map my gene after I get result from deseq2 .I want to convert all the ENSEMBL to gene name can you let me know how do I do that? ...
written 20 days ago by krushnach8090

Latest awards to krushnach80

Voter 3 months ago, voted more than 100 times.
Centurion 3 months ago, created 100 posts.
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: differential gene expression analysis
Supporter 4 months ago, voted at least 25 times.

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