User: RNAseqer

gravatar for RNAseqer
RNAseqer 20
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20
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New User
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Last seen:
14 hours ago
Joined:
1 month, 2 weeks ago
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z*****@gmail.com

Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.

Posts by RNAseqer

<prev • 19 results • page 1 of 2 • next >
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Filtering SNPS by minimum LD value in bcftools?
... Hello everyone, I have just started using bcftools to 'prune' some vcf files. While I have found some helpful examples of how to discard SNPs with high LD: bcftools +prune -l 0.6 -w 1000 frag.vcf -Ov -o output1.vcf I was hoping to actually create output where the SNPs kept were those ...
vcf bcftools vcftools ld r2 written 2 days ago by RNAseqer 20
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Comment: C: rowVars function, used in ballgown analysis not available for R 3.5.2, alternati
... This is going to save me some time and heartache. Thanks for the heads-up! ...
written 6 days ago by RNAseqer 20
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Comment: C: rowVars function, used in ballgown analysis not available for R 3.5.2, alternati
... Huh, must be! I tried to get it as part of matrixstats but that didnt work, this download did. Thanks a bunch! This was a real help. ...
written 17 days ago by RNAseqer 20
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rowVars function, used in ballgown analysis not available for R 3.5.2, alternatives?
... Hello, I've hit a bit of a snag here: I had to update to the latest version of R to get ballgown working, but one of the functions I see included in filtering out low expression genes, rowVars, is not available for this version of R. Using this tutorial: https://rpubs.com/kapeelc12/Ballgown Th ...
R ballgown rna-seq rowvars written 17 days ago by RNAseqer 20 • updated 16 days ago by kristoffer.vittingseerup1.6k
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Comment: C: ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls
... Good advice. I will be sure to do so. ...
written 17 days ago by RNAseqer 20
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Comment: C: ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls
... data_directory = system.file(Users/mylapple/Desktop/test_reads_folder_output/ballgown_inputs, package = 'ballgown') ?? ...
written 18 days ago by RNAseqer 20
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ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls: ballgown -> read.table -> file
... I have been running through the bioconductor introduction to ballgown and hit a snag in loading up the .ctab files using the method described therin. https://www.bioconductor.org/packages/devel/bioc/vignettes/ballgown/inst/doc/ballgown.html The instructions suggest that if you store your data in a ...
ballgown stringtie rna-seq written 18 days ago by RNAseqer 20
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No Sensitivity/Accuracy output from gffcompare, what am I doing wrong?
... Hello all, So, Im running a test dataset available here https://github.com/Arabinet/Introduction-to-Bioinformatics/wiki/Arabidopsis-RNA-Seq through an RNAseq pipeline I hope to use for experimental data later. I have recently been working with HISAT2 and STRINGTIE and have generated 18 gtf ...
precision accuracy gffcompare .stats. written 22 days ago by RNAseqer 20
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Can HISAT2 be invoked in bash shell, and can it be fed variables or names with wildcards as inputs?
... Hello all, So I have been trying to write up a .sh script that will automate the process of running HISAT2 on a bunch of paired end data. Since these are massive read files and physical memory on my computer is limited I have been writing a bash shell script that pulls read files off two at a time ...
hisat2 shell batch jobs wild cards bash written 4 weeks ago by RNAseqer 20 • updated 4 weeks ago by RamRS20k
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junction_annotation.py: How many 'novel' splice junctions/splice events are resonably expected from human RNA,
... Hello all, I was just wondering what a reasonable percentage of 'novel' splice junctions/splice events is for human RNAseq data using the program junction_annotation.py. I am new to RNAseq and just running some published human RNAseq data through my pipeline in order to familiarize myself with t ...
junction_annotation.py rna-seq human written 5 weeks ago by RNAseqer 20

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