User: KG

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KG10
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1 year, 4 months ago
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c*********************@gmail.com

Posts by KG

<prev • 7 results • page 1 of 1 • next >
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Comment: C: How to identify species specific genes?
... Thanks for correcting me! Could you please elaborate more specifically or guide me to proper reference where it is discussed in details? ...
written 27 days ago by KG10
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How to identify species specific genes?
... Hi, I have genomes (fasta files) of two species and the corresponding GFF3 files. I need to identify a. genes that are unique (< 30% similarity) to each species, b. highly conserved and c. highly diverged. Can you please suggest how I can do that? NB: these are eukaryotic genomes of ~15-16 Mb a ...
gene species specific gene blast written 27 days ago by KG10
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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 10 weeks 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 10 weeks 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 3 months 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 16 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 16 months ago by KG10

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