User: KG

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KG10
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3 months, 1 week ago
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3 years, 2 months ago
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Posts by KG

<prev • 12 results • page 1 of 2 • next >
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Comment: C: renaming fasta file with part of fasta header
... I have tried doing for i in *.faa; do mv $i $(head -1 $i | cut -f1 -d ' ' | tr -d '>' ).faa done This changed 'file.faa' to 'XP_003072227.1.faa' but I need 'Encephalitozoon intestinalis.faa'. How to modify the script? ...
written 4 months ago by KG10
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renaming fasta file with part of fasta header
... I have about 100 multiple fasta files (e.g., file.faa), which I have to rename with the species name mentioned in the fasta header. The fasta headers of these files are in the following format: >XP_003072227.1 aminopeptidase N [Encephalitozoon intestinalis ATCC 50506] How do I rename 'file ...
sed awk written 4 months ago by KG10 • updated 4 months ago by genomax91k
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Suggestion for uploading of NGS data and genome assembly
... Dear all, We have developed two genome assemblies using PacBio SMRT, Oxford nanopore, and Illumina sequence data. Now we need to upload the raw data and the genome assemblies to NCBI. However, I have not done this before. I tried the submission guideline but I am a bit confused about the GEO, Bio p ...
ncbi data submission ngs data upload written 12 months ago by KG10
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Comment: C: Improvement of genome assembly using illumina contigs and nanopore reads
... Thanks for your suggestions. I'll give it a try and use nanopore polishing tools. We have not generated that illumina assembly. It's available from NCBI, but not the raw reads. ...
written 16 months ago by KG10
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Improvement of genome assembly using illumina contigs and nanopore reads
... Hi, I have nanopore reads and a very fragmented genome assembly (~500 contigs for 16-20 mb genome) but not the illumina reads. I have used canu and generated a de novo assembly (44 contigs) from the nanopore reads (~30x). Since I do not have illumina reads, I could not polish this de novo assembly. ...
illumina nanopore scaffolding genome assembly written 16 months ago by KG10 • updated 16 months ago by h.mon31k
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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 23 months 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 23 months 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 2.1 years 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 2.1 years 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 2.1 years ago by KG10

Latest awards to KG

Popular Question 3 months ago, created a question with more than 1,000 views. For Genome annotation using transcriptome data
Popular Question 12 months ago, created a question with more than 1,000 views. For tRNA differential expression analysis in mRNA sequencing data

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