User: lshepard

gravatar for lshepard
lshepard140
Reputation:
140
Status:
Trusted
Location:
United States
Last seen:
2 days, 23 hours ago
Joined:
3 years, 11 months ago
Email:
l********@gmail.com

Posts by lshepard

<prev • 46 results • page 1 of 5 • next >
0
votes
0
answers
84
views
0
answers
Comment: C: Interpreting DEseq2 results
... To add to the above, it would also be useful to know if you are applying a minimum count cutoff per gene? Perhaps if you are applying a cutoff well above the default, it could be removing a certain number of genes (up and down-regulated), although of course removing low-expressing genes also has an ...
written 3 days ago by lshepard140
1
vote
2
answers
149
views
2
answers
Comment: C: Assembly database choice for RNA-seq and ChIP-seq
... Yes, that thought came to my mind, but they also mention other concerns about the GTF from Table Browser in the link above, so I think the option above may be a quicker way to resolve these other concerns: > * The Table Browser adds start and stop codon annotations whether or not the transcript ...
written 16 days ago by lshepard140
0
votes
2
answers
149
views
2
answers
Answer: A: Assembly database choice for RNA-seq and ChIP-seq
... Posting this solution to my question in case it helps anyone else since the current output of GTF from UCSC is a bit confusing (I am not sure why they still keep the GTF output as an option, given the work around below, but oh well): This is the solution I found to ensure that UCSC GTF contains dis ...
written 16 days ago by lshepard140
0
votes
2
answers
149
views
2
answers
Comment: C: Assembly database choice for RNA-seq and ChIP-seq
... To complement my comment, I wanted to point out that indeed I have seen previous BioStar post discussing this such as [this one][1] But in the end, there wasn't a conclusion about dealing with the transcript variants for RNA-seq gene-level analysis, which is relevant to my original question, if I w ...
written 21 days ago by lshepard140
0
votes
1
answer
129
views
1
answers
Answer: A: rna seq single ended -Information on Rseqc report
... This is unstranded RNAseq. You can tell by the almost equal distribution of reads explained by forward and reverse output. ...
written 21 days ago by lshepard140
0
votes
2
answers
149
views
2
answers
Comment: C: Assembly database choice for RNA-seq and ChIP-seq
... To clarify though, while indeed the version should be the same, both Ensembl (I focus on Ensembl, because Gencode is only for humans and mice) and UCSC have their own genome files. How much discrepancy is there between these genomes (they would still be the same version such as mm10 or rn6)? I am aw ...
written 21 days ago by lshepard140
1
vote
2
answers
149
views
2
answers
Assembly database choice for RNA-seq and ChIP-seq
... Hello, First, just a brief mention that this is indeed a topic that has been brought-up in the past, but I would like some more specific feedback. When comparing RNA-seq to ChIP-seq data, ideally, it would be great to use the same assembly and annotation files for both seqs. For any epigenetics wo ...
chip-seq rna-seq written 22 days ago by lshepard140
0
votes
1
answer
264
views
1
answers
Comment: C: Recommendation for statistics book
... Hmm may not covers all of your interested areas but the book below is very useful to general statistical concepts in bioinformatics. Worth taking a look (where most of it is shown in R): https://www.amazon.com/Data-Analysis-Life-Sciences-R-ebook-dp-B01N6Y3IVP/dp/B01N6Y3IVP/ref=mt_kindle?_encoding=U ...
written 5 months ago by lshepard140
0
votes
17
answers
33k
views
17
answers
Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Perhaps the Biostars Slack group would be ideal for this? You could request to create a channel for the book itself and then for the lectures. It is worth a try (maybe for a test period of time). ...
written 8 months ago by lshepard140
0
votes
1
answer
679
views
1
answers
Comment: C: TCGA RNASeq Data
... Just a general advice on TCGA data: I would recommend to analyze the data from scratch (fastq files which you can acquire by using Picard Tools), rather then the provided BAM files. This is the only way that you can be sure that proper QC is being performed. ...
written 11 months ago by lshepard140

Latest awards to lshepard

Popular Question 6 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Popular Question 9 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 14 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 14 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 19 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: which one is adapter and which one is index
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Rsubread installation issues

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2279 users visited in the last hour