User: Tommy Carstensen

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110
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Trusted
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United Kingdom
Twitter:
tommycarstensen
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2 weeks ago
Joined:
6 years, 6 months ago
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Posts by Tommy Carstensen

<prev • 51 results • page 1 of 6 • next >
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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 15 days ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110
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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 3 months ago by Tommy Carstensen110 • updated 3 months ago by genomax37k
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Comment: C: How to get gene name from coordinates using python.
... I get `TypeError: __init__() got an unexpected keyword argument 'auto_download'` ...
written 6 months ago by Tommy Carstensen110
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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 6 months ago by Tommy Carstensen110

Latest awards to Tommy Carstensen

Popular Question 8 weeks ago, created a question with more than 1,000 views. For web interface for getting rsID in dbSNP of some coordinate?
Voter 8 weeks ago, voted more than 100 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 8 months ago, created a question with more than 1,000 views. For Where can I download a list of mtDNA haplogroup mutations?
Popular Question 18 months ago, created a question with more than 1,000 views. For 1000G high coverage depth of sequencing?
Popular Question 24 months ago, created a question with more than 1,000 views. For mitochondrial variant calling
Scholar 2.2 years ago, created an answer that has been accepted. For A: Get start and end positions of transcripts via REST API?
Supporter 2.8 years ago, voted at least 25 times.

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