User: RNAseqer
RNAseqer • 20
- Reputation:
- 20
- Status:
- New User
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- Last seen:
- 14 hours ago
- Joined:
- 1 month, 2 weeks ago
- Email:
- z*****@gmail.com
Very new to RNAseq, previous experience in genome assembly, phylogenetic analysis, substitution rate analysis etc etc.
Posts by RNAseqer
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... 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 ...
written 2 days ago by
RNAseqer • 20
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... 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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... 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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5 follow
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... 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 ...
written 17 days ago by
RNAseqer • 20
• updated
16 days ago by
kristoffer.vittingseerup • 1.6k
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... Good advice. I will be sure to do so. ...
written 17 days ago by
RNAseqer • 20
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... 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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... 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 ...
written 18 days ago by
RNAseqer • 20
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... 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 ...
written 22 days ago by
RNAseqer • 20
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... 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 ...
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... 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 ...
written 5 weeks ago by
RNAseqer • 20
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