User: Tommy Carstensen

Reputation:
110
Status:
Trusted
Location:
United Kingdom
Twitter:
tommycarstensen
Last seen:
1 month, 2 weeks ago
Joined:
6 years, 3 months ago
Email:
b*******@tommycarstensen.com

Posts by Tommy Carstensen

<prev • 50 results • page 1 of 5 • next >
0
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110
0
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110
0
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110
0
votes
2
answers
2.8k
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 6 weeks ago by Tommy Carstensen110
0
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110
0
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110
7
votes
2
answers
237
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 6 weeks ago by Tommy Carstensen110 • updated 6 weeks ago by genomax33k
0
votes
5
answers
3.3k
views
5
answers
Comment: C: How to get gene name from coordinates using python.
... I get `TypeError: __init__() got an unexpected keyword argument 'auto_download'` ...
written 4 months ago by Tommy Carstensen110
0
votes
6
answers
10k
views
6
answers
Comment: C: Find Out The Genes That Correspond To My Coordinates
... Would it be possible to print the gene name `TMEM201` instead of `NM_001130924`? ...
written 4 months ago by Tommy Carstensen110
0
votes
3
answers
331
views
3
answers
Comment: C: get build 37 positions from dbSNP rsIDs
... If one wants to see all of the available columns, then do: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'show columns from snp147' ...
written 4 months ago by Tommy Carstensen110

Latest awards to Tommy Carstensen

Popular Question 6 months ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 6 months ago, created a question with more than 1,000 views. For Where can I download a list of mtDNA haplogroup mutations?
Popular Question 16 months ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 21 months ago, created a question with more than 1,000 views. For mitochondrial variant calling
Scholar 2.1 years ago, created an answer that has been accepted. For A: Get start and end positions of transcripts via REST API?
Supporter 2.6 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: 1670 users visited in the last hour