User: Tommy Carstensen

Reputation:
150
Status:
Trusted
Location:
United Kingdom
Twitter:
tommycarstensen
Last seen:
3 months ago
Joined:
7 years ago
Email:
b*******@tommycarstensen.com

Posts by Tommy Carstensen

<prev • 53 results • page 1 of 6 • next >
1
vote
8
answers
9.8k
views
8
answers
Comment: C: How To Generate A Bibtex File From Pmids
... I just wrote a Python 3 solution here: https://gist.github.com/tommycarstensen/ec3c57761f3846c339de925b66f4ac1b ...
written 3 months ago by Tommy Carstensen150
0
votes
8
answers
9.8k
views
8
answers
Comment: C: How To Generate A Bibtex File From Pmids
... @Nick This is great, but do you have it in Python 3 instead of Python 2? ...
written 3 months ago by Tommy Carstensen150
0
votes
5
answers
5.5k
views
5
answers
Answer: A: Lift-over on a VCF
... Picard LiftoverVcf, which is supported by the Broad: http://broadinstitute.github.io/picard/command-line-overview.html#LiftoverVcf ...
written 7 months ago by Tommy Carstensen150
0
votes
2
answers
857
views
2
answers
Comment: C: Best RNAseq spliced aligner?
... Thanks @genomax. I'll have a look at BBMap. It seems their emphasis is on sensitivity. To me accuracy/precision is equally important. I wonder why RNAseq aligners are being churned out, when STAR works so well. I think I'll just stick with STAR, which is tried and tested and has proved its worth. ...
written 10 months ago by Tommy Carstensen150
0
votes
2
answers
857
views
2
answers
Comment: C: Best RNAseq spliced aligner?
... Thanks for pointing me to that very recent review @prasundutta87! I'll have a look. I think I'll stick with STAR, because it gives me a vastly superior alignment rate compared to HISAT2; i.e. well above 90%. ...
written 10 months ago by Tommy Carstensen150
0
votes
2
answers
857
views
2
answers
Comment: C: Best RNAseq spliced aligner?
... Thanks for pointing me to Hera. It sure seems to be fast. I've just asked them, if they have measures of accuracy and precision relative to STAR. That's more important to me than incremental speed gains. ...
written 10 months ago by Tommy Carstensen150
0
votes
2
answers
4.0k
views
2
answers
Comment: C: Hera: A new tool for RNA-Seq analysis
... What is the accuracy and precision of Hera compared to STAR on simulated sets with short anchors and indels? Thanks. ...
written 10 months ago by Tommy Carstensen150
0
votes
2
answers
857
views
2
answers
Comment: C: Best RNAseq spliced aligner?
... Those are all the default settings. I just prefer writing them explicitly, so I can reproduce my results, if the defaults are changed. I stripped away all the options except for `--known-splicesite-infile` and still got the same results. With STAR I get an alignment rate well above 90%. ...
written 10 months ago by Tommy Carstensen150
0
votes
2
answers
857
views
2
answers
Comment: C: Best RNAseq spliced aligner?
... Thanks a lot @WouteDeCoster! I'll just stick with STAR then. I don't think my coverage is quite good enough for alignment/reference free approaches. Thanks! ...
written 10 months ago by Tommy Carstensen150
7
votes
2
answers
857
views
2
answers
Best RNAseq spliced aligner?
... I've run the RNA-seq alignment software HISAT2 on 75bp PE reads in fastq files like this: hisat2 \ -q \ --phred33 \ --n-ceil L,0,0.15 \ --pen-cansplice 0 \ --pen-noncansplice 12 \ --pen-canintronlen G,-8,1 \ --pen-noncanintronlen G,-8,1 \ --min-int ...
alignment rna-seq sequencing written 10 months ago by Tommy Carstensen150 • updated 10 months ago by genomax49k

Latest awards to Tommy Carstensen

Popular Question 4 months ago, created a question with more than 1,000 views. For web interface for getting rsID in dbSNP of some coordinate?
Popular Question 8 months ago, created a question with more than 1,000 views. For web interface for getting rsID in dbSNP of some coordinate?
Voter 8 months ago, voted more than 100 times.
Popular Question 15 months ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 15 months ago, created a question with more than 1,000 views. For Where can I download a list of mtDNA haplogroup mutations?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For mitochondrial variant calling
Scholar 2.8 years ago, created an answer that has been accepted. For A: Get start and end positions of transcripts via REST API?
Supporter 3.4 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1677 users visited in the last hour