User: rrbutleriii

gravatar for rrbutleriii
rrbutleriii50
Reputation:
50
Status:
New User
Location:
US, Chicago
Twitter:
@rrbiiiphd
Scholar ID:
Google Scholar Page
Last seen:
1 day, 6 hours ago
Joined:
8 months, 4 weeks ago
Email:
r**********@gmail.com

Posts by rrbutleriii

<prev • 14 results • page 1 of 2 • next >
1
vote
1
answer
89
views
1
answers
Answer: A: From coverageBed to a list of reads per genes
... The reason the bam file is not working is because the bed file doesn't contain enough information to re-create reads. Perhaps there is a tool that attempts to reconstruct reads based on coverage beds, but that sounds...not good. You need a true bam/sam for featureCounts. I am unfamiliar with the ac ...
written 6 days ago by rrbutleriii50
0
votes
1
answer
116
views
1
answers
Answer: A: Questions about gene length and GC content in CQN normaliztion
... See this [post](https://www.biostars.org/p/317962/) for question one and two. Specifically, if all you need is gene length and GC, and you don't want to learn to access biomaRt directly, this will work (but takes a little time depending on the size of you matrix). library (EDASeq) ensembl_ ...
written 7 days ago by rrbutleriii50
1
vote
1
answer
187
views
1
answers
Comment: C: comparing RNA seq data from different studies using ratios
... The literal answer to 'would the ratio differ' is quite possibly. Thus my above that quantile normalized data shouldn't be compared in this way. Quantile normalization is not the same as the other normalization concepts of TPM/FPKM/RPKM. And even for those it is not recommended to compare across t ...
written 4 weeks ago by rrbutleriii50
0
votes
0
answers
127
views
0
answers
Pre-filtering transcriptome data by gene type
... I have seen in some transcriptome comparison analyses that the total RNA-seq data set is pre-filtered to only include protein-coding genes, or to exclude pseudogenes, or "short RNAs" ([Schwartzentruber et al](https://www.nature.com/articles/s41588-017-0005-8)). In a sense I understand this to imply ...
rna-seq non-coding rna transcriptome written 4 weeks ago by rrbutleriii50
2
votes
3
answers
274
views
3
answers
Answer: A: PacBio sequencing for variant calling?
... tl;dr The question to ask is the type of variation you are expecting to encounter; a non-systematic approach to be sure, but there is not a one size fits all solution. In my personal experience (TruSeq/Nextera Illumina several paired end types de novo and reference based, PacBio RSII p4c2/p5c3/p6c4 ...
written 4 weeks ago by rrbutleriii50
0
votes
1
answer
187
views
1
answers
Answer: A: comparing RNA seq data from different studies using ratios
... Read more in https://www.biostars.org/p/314454/ "The upper quartile FPKM (FPKM-UQ) is a modified FPKM calculation in which the total protein-coding read count is replaced by the 75th percentile read count value for the sample." https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mR ...
written 5 weeks ago by rrbutleriii50
0
votes
0
answers
233
views
0
answers
Comment: C: Windows batch cmd for fastq-dump
... Indeed I have. This gets deep into the weeds of our institutional politics (of the type that would make Kafka blush). The short of it is this the actual server is airgapped, and virtual machine with internet access for the purposes of shuttling data is this one (a Win Server 2008 R2 OS, with heavily ...
written 8 weeks ago by rrbutleriii50
0
votes
2
answers
183
views
2
answers
Answer: A: SRA prefetch error
... This may be a temporary system outage, see: https://github.com/ncbi/sra-tools/issues/84. Otherwise, based on the timeout and failed SSL handshake I wouls suspect a firewall connection issue. Do you normally connect via a proxy on your network? ...
written 8 weeks ago by rrbutleriii50
0
votes
0
answers
233
views
0
answers
Comment: C: Windows batch cmd for fastq-dump
... Wouldn't you believe the silliness of the situation, this machine also only has Internet Explorer, and won't allow java (or aspera connect). I would batch query the fastq files via ftp, but I want to verify file integrity after download using vdb-validate, as I had heard of incomplete transfers of f ...
written 9 weeks ago by rrbutleriii50
0
votes
0
answers
124
views
0
answers
Uncertain about using cqnplots for quality control
... When doing quantile normalization of RNA-seq data using cqn. The vignette examines the output using `cqnplot` to generate two graphs, but doesn't go into detail as to what to look for in terms of issues with the normalization. In this data, there appear to be three samples that don't follow the same ...
R rna-seq cqn written 9 weeks ago by rrbutleriii50

Latest awards to rrbutleriii

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 691 users visited in the last hour