User: Geparada
Geparada • 1.4k
- Reputation:
- 1,390
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- Trusted
- Location:
- Cambridge
- Website:
- http://bit.ly/1Mg7ioR
- Last seen:
- 22 hours ago
- Joined:
- 7 years, 10 months ago
- Email:
- g*******@uc.cl
PhD student at Welcome Trust Sanger Institute.
https://twitter.com/ge_parada
Posts by Geparada
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... cool! very simplified, thanks ! :) ...
written 7 weeks ago by
Geparada • 1.4k
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... I would do something like:
samtools view file.bam | awk '($6 ~ /D/) && ($5>10)'
`($6 ~ /D/)` means "deletion in CIGAR" and `$5>10` means MAPQ>10
I really like awk oneliners for doing quick filters like this.
...
written 9 weeks ago by
Geparada • 1.4k
1
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1
answer
152
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Answer:
A: RNA Splicing databases
... In general you can find the splice sites from gene models such as GENCODE (https://www.gencodegenes.org/), refseq or UCSC genes. I particularly recommend you to use GENCODE since is constantly getting improved. You can extract splicing sites from GTF, GFF or bed12 files. If you use UCSC Table Brows ...
written 9 weeks ago by
Geparada • 1.4k
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... "A comprehensive survey of non-canonical splice sites in the human transcriptome" If you have any questions let me know. ...
written 9 weeks ago by
Geparada • 1.4k
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1
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344
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1
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... Have you tried to change the internet browser? In chrome should be working just by drag-and-click. Are you working logged into your account? have you tried to log-out? just to check if this is really a setting that you configured in your account? ...
written 12 months ago by
Geparada • 1.4k
0
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1
answer
852
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... According with the Rsem paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323) building the transcript should be possible if you just input the transcript sequence as fasta. However this is not working for me either. An error with rsem-synthesis-reference-transcripts s ...
written 12 months ago by
Geparada • 1.4k
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... Hi to all,
I recently gave a lab meeting and I said that approximately one third of the transcriptome is targeted by non-sense mediated decay (NMD). I used to read a lot about NMD, but I don't really remember where I took that number from, or even if it's true hahaha
However in plant at least 17.4 ...
written 2.1 years ago by
Geparada • 1.4k
3
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6
answers
5.7k
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6
answers
Answer:
A: HISAT2 or Tophat2
... 1.-Do not use Tophat2. Nowadays you have many much better options, just look a the bechmarks.
2.- STAR it is pretty good, I would totally recommend it. However the issue with STAR is the high memory requirement. If you are working with human and you have less than 28 GB of RAM memory, you should us ...
written 2.2 years ago by
Geparada • 1.4k
2
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... I'm glad you find useful :) Currently there is no pdf version available, but it is a good idea. Now if you know a bit of R/Rstudio/Rmd you can generate the pdf from your own if you clone this git https://github.com/hemberg-lab/scRNA.seq.course and then open the Rproject file. Using knit you can gene ...
written 2.7 years ago by
Geparada • 1.4k
20
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3.5k
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Tutorial:
Analysis of single-cell RNA-seq data
... Hello everyone!
If you are interested into analice single cell RNA-seq data, I highly recommend you to take a look to this [course][1] which was developed in our lab. This material correspond to a one-day training course which it's given at University of Cambridge. As a student, is one of the best ...
written 2.7 years ago by
Geparada • 1.4k
Latest awards to Geparada
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6 weeks ago,
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For What Script (Or Program) Should I Use To Filter Low Complexity And Repetitive Reads From Rna-Seq?
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12 months ago,
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For A: What Databases Are Available For Rna-Seq Datasets?
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For How To Merge Overlapping Two Or More Dna Sequence?
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For A: Error Invoking Makeblastdb
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For How To Merge Overlapping Two Or More Dna Sequence?
Teacher
2.0 years ago,
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For A: Searching 200-400Bp Matches Against Mammalian Genome (~Human-Mouse Distance)
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created a question with more than 5,000 views.
For How To Merge Overlapping Two Or More Dna Sequence?
Teacher
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created an answer with at least 3 up-votes.
For A: Error Invoking Makeblastdb
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created a question with more than 1,000 views.
For Memory leak while reading a bigwig in python
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For How To Merge Overlapping Two Or More Dna Sequence?
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For Fastq Splitter For Paired End Reads
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2.6 years ago,
created a question with more than 10,000 views.
For How To Merge Overlapping Two Or More Dna Sequence?
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For Gencode Gtf To Bed12 Or Psl
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For Mapping Trimmed Paired End Reads With Mapsplice
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For How To Merge Overlapping Two Or More Dna Sequence?
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Getting The Error Probability Statistics From A (Large) Fastq File
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For Mapping Trimmed Paired End Reads With Mapsplice
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3.1 years ago,
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For Which Useful Debian-Like Repositories Do You Know?
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