User: KG

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KG10
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2 days, 18 hours ago
Joined:
1 year, 2 months ago
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c*********************@gmail.com

Posts by KG

<prev • 5 results • page 1 of 1 • next >
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Answer: A: error while Kissplice run
... Dear Leandro, Thanks for replying! I had paired ended RNAseq reads (~30 million) which I aligned on the reference genome using STAR, generated a coordinate sorted bam file. Next, I have converted bam to sam and used kisspliceref2genome to call the SNPs. I am now following the pipeline explained i ...
written 19 days ago by KG10
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error while Kissplice run
... I am using kissplice to identify SNPs from the transcriptome data. I am getting an error. This is how my terminal looks like: kissplice2refgenome -o Ct_SNP --pairedEnd PAIREDEND --vcf /home/mml/KG/Ct_STAR1.sam Run starts... Processing mapping information... Traceback (most recent call last): Fil ...
kissplice snp transcriptome written 20 days ago by KG10
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Genome annotation using transcriptome data
... Hi, We have generated a newer version of genome assembly for a yeast species. We have also sequenced the transcriptome. Now we would like to annotate the genome. My questions are: 1. How to use the transcriptome data for annotation? 2. Can you recommend a pipeline for genome annotation which use ...
genome annotation transcriptome written 6 weeks ago by KG10
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Answer: A: tRNA differential expression analysis in mRNA sequencing data
... Thank you, Carlo! That is an excellent suggestion. I am planning to check for a couple of tRNAs for which the raw read counts are high and have log2FC lower than -4.0. I have done Southern blotting experiments, but not done northern blotting experiments myself. I understand northern blotting procedu ...
written 14 months ago by KG10
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tRNA differential expression analysis in mRNA sequencing data
... Hi, I have analysed an mRNA sequencing dataset (~30 million reads for each of the two biological replicates per sample for two samples, generated from poly-A enrichment library) using STAR-Featurecounts-EdgeR protocol. I see 110 tRNA genes are differentially expressed in my mutant compared to contr ...
poly-a enrichment linrary mrna seq trna written 14 months ago by KG10

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