User: Mike

gravatar for Mike
Mike30
Reputation:
30
Status:
New User
Location:
Canada
Last seen:
12 hours ago
Joined:
2 years, 9 months ago
Email:
M*******@outlook.com

Posts by Mike

<prev • 8 results • page 1 of 1 • next >
0
votes
1
answer
125
views
1
answer
geom_point, indicate data points outside plot
... On this plot, data points that are outside the limits of the plot are pointed to using triangles: https://i.imgur.com/ScTCGMw.png from http://www.bioconductor.org/help/workflows/rnaseqGene/#ma-plot Is it possible to do something similar using ggplot2 (geom_point)? Thank you. ...
geom_point written 12 weeks ago by Mike30 • updated 12 weeks ago by russhh3.5k
0
votes
2
answers
511
views
2
answers
Answer: A: Different coverage on RNA-Seq strands
... I think I'm having the same problem. I'm using bamCoverage (version 3.0.0) on my paired-end stranded RNA-seq using the --filterRNAstrand option and for each file due to filtering ~90% are being used for the forward strand and ~5% for the reverse, which I don't think is correct. Were you able to figu ...
written 3 months ago by Mike30
0
votes
2
answers
555
views
2
answers
Answer: A: peak detection: different q-value for different experiments?
... I don't know if it's the most ideal way to do it but yes I've done it. I would use the same cutoff if it's for 2 samples I want to directly compare to each other (like protein X in treated vs untreated) because hopefully the samples you want to compare worked equally well otherwise it's not a fair c ...
written 14 months ago by Mike30
1
vote
1
answer
486
views
1
answers
Answer: A: looking for normal cancer WGBS data
... If you search ENCODE for WGBS, Homo sapiens, and mammary gland there are 7 results (though they have some warnings, could just be a metadata issue): https://www.encodeproject.org/search/?type=Experiment&replicates.library.biosample.donor.organism.scientific_name=Homo+sapiens&organ_slims=mam ...
written 14 months ago by Mike30
1
vote
2
answers
894
views
2
answers
Answer: A: What's the name in RepeatMasker for mouse major satellite repeats?
... I believe that "GSAT_MM" in RepeatMasker are supposed to be major satellites (see below) but if you look at the locations of all the GSAT_MM repeats they aren't all near centromeres. It's possible that the coordinates just aren't available for all the major satellite repeats: since major satellites ...
written 14 months ago by Mike30
0
votes
0
answers
519
views
0
answers
Assigning RepeatMasker classes and families to Repbase repeats
... I'm using mouse mm10. The RepeatMasker track on the UCSC Genome Browser categorizes each repeat with a name, class, and family (there are ~1500 different repeat names, 10 classes and ~50 families). RepBase uses an ID and one or more keywords. I know there's not a one to one relationship between the ...
repeats repeatmasker repbase written 15 months ago by Mike30
1
vote
1
answer
1.7k
views
1
answers
Answer: A: Intron-aware coverage for paired-end RNA-seq data.
... It sounds like what you want to do is convert an aligned .sam file to a wiggle/bedgraph file, is this correct?  The STAR RNA alignment program has an option to do this but I haven't used it. ...
written 2.7 years ago by Mike30
0
votes
2
answers
2.0k
views
2
answers
Comment: C: A puzzling warning when running Cufflinks
... The gene lines in annotation files seem to cause problems with cufflinks, you can try removing them: Remove "gene" entries (this is what I use) https://groups.google.com/d/msg/tuxedo-tools-users/FTKA4qozJIc/p47AwnCXxvwJ Remove everything except "exon" entries: https://groups.google.com/d/msg/tuxed ...
written 2.7 years ago by Mike30

Latest awards to Mike

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: 1701 users visited in the last hour