User: harishk0201

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harishk020170
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Posts by harishk0201

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Answer: A: extract single contig from fasta file based on name?
... The easiest way is to do the following, but ofcourse as ATpoint points out, we don't know how your contig headers look, so that may be an issue. The easiest way is however below: `printf "contigid\n" | seqtk subseq contigs.fasta - > contigid.fasta` ...
written 7 weeks ago by harishk020170
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Answer: A: whole genome alignment using nucmer
... You can use dnadiff from the MUMmer suite actually. It will generate a .report file where all the details are present. ...
written 19 months ago by harishk020170
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Comment: C: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
... Lately I have been following the methods listed here: - BUSCO/CEGMA for checking the core genes - Map RNASeq reads and unigenes dervied from transcriptome assembly - Map Proteins from closely related species - Map constituent reads that were used to form the assembly and check their depth and m ...
written 2.4 years ago by harishk020170
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Answer: A: Longer scaffolds from multiple eukaryote genome assemblies
... Hey Eric, Try Quickmerge : https://github.com/mahulchak/quickmerge But are you sure that these genomes are in Gbs rather than Mbs? Seems a bit tad too much. You can try HaploMerger2 as well. ...
written 2.8 years ago by harishk020170
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Answer: A: annotation of SV (structural variants)
... I tend to generally use intansv. [link for the R Package][1] You'll need to create a custom tab delimited annotation file for it, but its really easy! [1]: https://bioconductor.org/packages/release/bioc/html/intansv.html ...
written 2.9 years ago by harishk020170
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Comment: C: Augustus/Maker2 failing due to invalid nucleotides in sequence
... No, its the 8th contig. I picked one out of the blue to check if there was something wrong in the contigs. I've added it to the post, should have done that in the first place. Thanks for the help! ...
written 3.2 years ago by harishk020170
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Comment: C: Augustus/Maker2 failing due to invalid nucleotides in sequence
... Yes I did! I don't know what is the reason behind the error though. ...
written 3.2 years ago by harishk020170
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Augustus/Maker2 failing due to invalid nucleotides in sequence
... Hi! I'm trying to annotate genome using Maker. So far, I have the gene predictions using genemark, a repeat masked GFF and augustus trained model. Now when I'm trying to run Maker2, I have the following error: /apps/busco/augustus-3.2.3/bin/augustus: ERROR Invalid nucleotide '�' encountered. /ap ...
augustus assembly maker2 annotation written 3.2 years ago by harishk020170
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SNP calling from a DeNovo genome assembly
... Hi, I have around 50 genotypes of a pant species with two parents.I would like to perform a SNP genotyping analysis. I have a few questions in this regard. 1. For SNP calling from essentially a draft genome (apple) and to observe variation from both the parents, would I need to co-assemble them o ...
genome snp written 4.6 years ago by harishk020170
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Answer: A: Reg: Changing outliers in RNASEQ
... For pairwise correlation, the absolute values for correlation range from 0.75-0.9 for the confounding sample and rest are from 0.85-1. I removed the confounding sample and the range for all the samples (sort of a pooled correlation heatmap) went from 0.2-1 to 0.6-1, which makes me wonder whether th ...
written 4.7 years ago by harishk020170

Latest awards to harishk0201

Popular Question 19 months ago, created a question with more than 1,000 views. For Reg: Changing outliers in RNASEQ
Popular Question 19 months ago, created a question with more than 1,000 views. For Augustus/Maker2 failing due to invalid nucleotides in sequence
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: whole genome alignment using nucmer
Popular Question 2.2 years ago, created a question with more than 1,000 views. For SNP calling from a DeNovo genome assembly

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