User: k.kathirvel93
k.kathirvel93 • 140
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Posts by k.kathirvel93
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C: miRNA mRNA interaction studies
... Your .gtf annotation file, must have the gene names. Please ensure that. ...
written 3 days ago by
k.kathirvel93 • 140
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C: miRNA mRNA interaction studies
... Use `-g gene_name ` instead of `gene ID` while running featureCounts then go for DESeq2. ...
written 3 days ago by
k.kathirvel93 • 140
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C: miRNA mRNA interaction studies
... I am telling this based on the understanding of your Aim. Though you need to perform miRNA-mRNA interaction, next you have to do a target gene prediction of your miRNAs and correlate them with your DE genes from mRNA analysis results. Then go for an Gene enrichment and pathway analysis. ...
written 4 days ago by
k.kathirvel93 • 140
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... Thanks for the answers everyOne. So, what will be the solution to come up with a correct DE analysis with single data without replicates. ...
written 5 days ago by
k.kathirvel93 • 140
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... Hi EveryOne,
I have a miRNA-seq data (One Control and One infected) from my own study. All Downstream analysis tools like edgeR and DESEQ2 (except NoiSeq) Needs Triplicates. But in my case i have only one sample from control and infected, so i have duplicated twice the same gene counts for control ...
written 5 days ago by
k.kathirvel93 • 140
• updated
5 days ago by
giovannaventola3es9 • 10
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... It doesn't matter which aligner, its looks like a BAM file. Can you do featurecounts with your Bam file and extract the read counts. One more thing, if you want to use DESEQ2 for DE you have to have a replicates, but you said you have two samples, so better to go with Noiseq. ...
written 29 days ago by
k.kathirvel93 • 140
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Comment:
C: BLAST all against all
... I think you have a prob with your -subject myseq.fasta ( i hope this file is refefence). Try to use blastDB and create database from all reference protein seq files. you can create single alias file for your database. then repeat your command with -db parameter instead of -subject. Thanks ...
written 4 weeks ago by
k.kathirvel93 • 140
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142
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Comment:
A: Primer design from mapping file ?
... Can you tell the purpose of primers ? ...
written 4 weeks ago by
k.kathirvel93 • 140
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... Sorry for the confusion i have modified the post now. Thanks. ...
written 5 weeks ago by
k.kathirvel93 • 140
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Comment:
C: SRA files bulk downloads
... What is that ERR688040 ? Is that ID correct? and why don't you try .sh script with fastqdump. ...
written 5 weeks ago by
k.kathirvel93 • 140
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