User: Geparada

gravatar for Geparada
Geparada1.4k
Reputation:
1,390
Status:
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

<prev • 135 results • page 1 of 14 • next >
0
votes
3
answers
6.6k
views
3
answers
Comment: C: How to determine if SRA file is single or paired end?
... cool! very simplified, thanks ! :) ...
written 7 weeks ago by Geparada1.4k
1
vote
3
answers
246
views
3
answers
Answer: A: Filtering sam/bam by using CIGAR deletion sites
... 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 Geparada1.4k
1
vote
1
answer
152
views
1
answers
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 Geparada1.4k
0
votes
1
answer
3.4k
views
1
answers
Comment: C: How The Non-Canonical Intron Splice Sites Came Out?
... "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 Geparada1.4k
0
votes
1
answer
344
views
1
answers
Comment: C: Question on UCSC genome browser display
... 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 Geparada1.4k
0
votes
1
answer
852
views
1
answers
Comment: C: rsem-prepare-reference and mouse mm9 genome reference files
... 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 Geparada1.4k
0
votes
0
answers
522
views
0
answers
What is the proportion of transcripts that are targeted by NMD on vertebrates genomes?
... 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 ...
gene expresion bionumber rna-seq written 2.1 years ago by Geparada1.4k
3
votes
6
answers
5.7k
views
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 Geparada1.4k
2
votes
0
answers
3.5k
views
0
answers
Comment: C: Analysis of single-cell RNA-seq data
... 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 Geparada1.4k
20
votes
0
answers
3.5k
views
0
answers
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 ...
single-cell tutorial rna-seq written 2.7 years ago by Geparada1.4k

Latest awards to Geparada

Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: What Databases Are Available For Rna-Seq Datasets?
Great Question 12 months ago, created a question with more than 5,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Good Answer 2.0 years ago, created an answer that was upvoted at least 5 times. For A: Error Invoking Makeblastdb
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: Error Invoking Makeblastdb
Epic Question 2.0 years ago, created a question with more than 10,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: HISAT2 or Tophat2
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Searching 200-400Bp Matches Against Mammalian Genome (~Human-Mouse Distance)
Great Question 2.0 years ago, created a question with more than 5,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Error Invoking Makeblastdb
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Memory leak while reading a bigwig in python
Great Question 2.1 years ago, created a question with more than 5,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Flag In Sam Format
Scholar 2.1 years ago, created an answer that has been accepted. For A: HISAT2 or Tophat2
Prophet 2.6 years ago, created a post with more than 20 followers. For Fastq Splitter For Paired End Reads
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Error Invoking Makeblastdb
Epic Question 2.6 years ago, created a question with more than 10,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Gencode Gtf To Bed12 Or Psl
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mapping Trimmed Paired End Reads With Mapsplice
Great Question 2.9 years ago, created a question with more than 5,000 views. For How To Merge Overlapping Two Or More Dna Sequence?
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: Error Invoking Makeblastdb
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
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Mapping Trimmed Paired End Reads With Mapsplice
Good Question 3.1 years ago, asked a question that was upvoted at least 5 times. For Which Useful Debian-Like Repositories Do You Know?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Error Invoking Makeblastdb

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1861 users visited in the last hour