User: k.kathirvel93

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Posts by k.kathirvel93

<prev • 98 results • page 1 of 10 • next >
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Comment: C: RNA-seq : Quantification problem after mapped with BBMap
... where should I use this `trimreaddescriptions=t` option? Thanking you ...
written 2 days ago by k.kathirvel9370
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How can i get gene name instead of gene ID from prepDE.py after STRINGtie?
... Hi EveryOne, I am trying STRINGtie for RNA-seq mRNA quantification after mapping with hisat2. STRINGtie can't produce gene raw counts, so i have used prepDE.py script to obtain gene counts. But, here i am getting only ensembl ID. I want gene name instead of ID. Any solution ? Thanks in advance. ...
gene next-gen rna-seq written 7 days ago by k.kathirvel9370
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How can I perform Differential expression analysis with just one control and one cancer sample?
... Hi EveryOne, Now i am in a situation to perform Differential gene expression analysis with just one control and one cancer sample. But, edgeR and DESeq2 will ask atleast two samples for control and cancer alone. What and How i can do now. Any suggestions. Thanks . ...
gene R rna-seq written 15 days ago by k.kathirvel9370
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RNA-seq : Quantification problem after mapped with BBMap
... Hi EveryOne, I have used BBMap for RNA-seq reads mapping. After mapping, i tried HTSeq, FeatureCounts and STRINGtie for quantification. But, i didn't get any results from featureCounts and HTSeq (readcount for all genes 0), STRINGtie showing that " your gtf file doesn't matched with your reference ...
software error next-gen rna-seq written 16 days ago by k.kathirvel9370 • updated 16 days ago by michael.ante2.6k
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How to convert transcript level TPM to gene level TPM ?
... Hi EveryOne, I am using various quantification tools for RNA-seq analysis. Now my query is : HTseq-count and featurecounts are producing gene level counts of gene abundance, STRINGtie and Express are producing in transcript level TPM abundance. Now i want to compare these two outputs. For this i a ...
gene next-gen rna-seq sequencing written 18 days ago by k.kathirvel9370 • updated 18 days ago by vj360
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Comment: C: Sort and convert the SAM files to BAM
... Try this samtools sort myfile.bam -o myfile_sorted.bam ...
written 18 days ago by k.kathirvel9370 • updated 18 days ago by finswimmer4.4k
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Comment: C: Need suggestions for RNA-seq quantification tools benchmarking.
... My aim is differential expression analysis ...
written 23 days ago by k.kathirvel9370
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Comment: C: RNA-seq mapping Reference genome
... My aim is differential gene expression analysis. I want to use both of the tools for comparison. Can i get the code for HIsat2 indexing with both genome(.fa) and annotation(.gtf) reference? Thanks. ...
written 24 days ago by k.kathirvel9370
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Comment: C: RNA-seq mapping Reference genome
... I am doing Transcriptome analysis. Draft genome - sequenced from patient sample. genome(.fa) - GRCh38 genome reference fasta file. Very clearly, STAR is taking .gtf and genome.fa file for reference mapping. But HISAT2 is taking only genome.fa as reference. Which one is correct. Thanks ...
written 24 days ago by k.kathirvel9370
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RNA-seq mapping Reference genome
... Hi EveryOne, I am using STAR and HISAT2 and two more tools RNA-seq data analysis. My question is, should I align my Draft genome with GRCh38 (.gtf) reference annotation or genome (.fa)reference? Which one is best? ...
next-gen rna-seq written 24 days ago by k.kathirvel9370 • updated 24 days ago by Devon Ryan82k

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