User: enxxx23
enxxx23 • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- European Union
- Last seen:
- 5 months, 2 weeks ago
- Joined:
- 6 years ago
- Email:
- e******@gmail.com
Posts by enxxx23
<prev
• 52 results •
page 1 of 6 •
next >
0
votes
4
answers
9.8k
views
4
answers
... This implementation looks like it will run very slow when reading a very large FASTQ file (with 200 million reads). A dictionary and a user-defined Python function is called for every single read.
Here is a more efficient and fast implementation of a FASTQ reader in Python.
https://github.com/lh3/r ...
written 5 months ago by
enxxx23 • 230
1
vote
2
answers
733
views
2
answers
... One way to do get more information about a fusion transcript found only by one tool would be to google (or search pubmed or google scholar?) the fusion gene and see where that fusion has been reported previously and in what type of cancers. If that fusion has been published previously in articles/da ...
written 11 months ago by
enxxx23 • 230
1
vote
2
answers
733
views
2
answers
... Different tools use different versions/sources of gene annotations and different genome releases/patches (eg. hg18/hg19). Therefore, as one would expect, one gets different results. I would say the the differences in Venn diagram can be explained mostly by differences in gene annotations uses (e.g. ...
written 11 months ago by
enxxx23 • 230
0
votes
2
answers
26k
views
2
answers
... It looks like CPM is computed here.
TPM for a gene should be computed using the TPMs computed from transcripts.
It looks like a big confusion is going on regarding CPM, TPM for genes, and TPM for transcripts. ...
written 12 months ago by
enxxx23 • 230
0
votes
1
answer
734
views
1
answers
... True, I should have mentioned the target organisms, which in this case are eukaryotes.
Retroviruses do not have RNA so doing RNA-seq on retroviruses is the only choice! ;-) ...
written 14 months ago by
enxxx23 • 230
0
votes
1
answer
734
views
1
answers
... BWA MEM is not a RNA-seq aligner by design. ...
written 14 months ago by
enxxx23 • 230
7
votes
1
answer
734
views
9 follow
1
answer
... What is the fastest (non-pseudo) aligner for RNA-seq illumina seq data today in year 2019?
...
written 14 months ago by
enxxx23 • 230
• updated
14 months ago by
kristoffer.vittingseerup • 3.2k
0
votes
2
answers
716
views
2
answers
... I totally agree! Do not use TopHat(2)! ...
written 17 months ago by
enxxx23 • 230
1
vote
2
answers
994
views
2
answers
... It would be great to have more info here, like for example:
- number of replicates,
- info about the times points (e.g. before and after the treatment time points?)
- type of disease: cancer or non-cancer
- tissues of origin for the samples (are all from the same tissue?),
- is there healthy tissue ...
written 17 months ago by
enxxx23 • 230
0
votes
2
answers
6.4k
views
2
answers
Comment:
C: Best tool for variant calling
... I concurr. This is my experience too.
What version of samtools are you using? ...
written 18 months ago by
enxxx23 • 230
Latest awards to enxxx23
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Public RNA-seq dataset for human & 2x250bp or longer
Teacher
5.0 years ago,
created an answer with at least 3 up-votes.
For A: The new era of bioinformatics: simple and fast tools, fewer and more informative
Commentator
5.5 years ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologists are reinventing the wheel for
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 985 users visited in the last hour