User: harishk0201

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harishk020120
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Posts by harishk0201

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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 3 months ago by harishk020120
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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 8 months ago by harishk020120
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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 9 months ago by harishk020120
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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 13 months ago by harishk020120
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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 13 months ago by harishk020120
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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 13 months ago by harishk020120
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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 2.5 years ago by harishk020120
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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 2.6 years ago by harishk020120
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Reg: Changing outliers in RNASEQ
... Hi all, I'm performing an experiment using RNA-seq data which will subsequently involve Differential Gene Analysis, and I'm experiencing the following problem. I'm using the **trinity rna-seq suite**, I've used kallisto as well as RSEM to check the replicate correlation. The species is crocodilian ...
kallisto rsem rna-seq written 2.6 years ago by harishk020120

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