User: IP

gravatar for IP
IP530
Reputation:
530
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
13 hours ago
Joined:
2 years, 6 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 99 results • page 1 of 10 • next >
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Comment: C: Insert mutations in a reference genome from a vcf
... I have test this tool, and it is doing (ultrafastly!) what I was looking for. Thanks! ...
written 1 day ago by IP530
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Insert mutations in a reference genome from a vcf
... Hi Biostars, I am looking for a tool to introduce variants in a reference genome. **The ideal tool I am looking for:** *Takes as input:* - genome fasta - a vcf file *What it does:* - Insert some of the variants (randomly) present in the vcf into the reference genome *What is the output* ...
simulation snp sequencing written 1 day ago by IP530 • updated 1 day ago by WouterDeCoster36k
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Comment: C: Differential expression: replicates in one condition, no replicates in the other
... Hi, thanks for the answer! that was actually what I finished doing. I had a 4 biological replicates for the "healthy" group and think that things worked fine cheers, ...
written 21 days ago by IP530
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... -A fai file is a index on the fasta file with the format specified [here][1] -Bowtie2 output is the Burrows-Wheeler transformation of the reference genome. You can read about the BW transform [ here][2]. They are two different indexing techniques, so bowtie2-build does create a fai file because it ...
written 9 weeks ago by IP530
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Comment: C: common CNVs among multiple files
... bedtools multiinter will help you ...
written 11 weeks ago by IP530
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Answer: A: Error correction of long reads
... Thanks to this [answer][1] in bioinformatics stackexchange, there is a tool doing exactly what you want. The tool is called [C3P0a][2] [1]: https://bioinformatics.stackexchange.com/questions/5397/error-correction-within-the-long-read/5406#5406 [2]: https://github.com/rvolden/C3POa ...
written 3 months ago by IP530
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Comment: C: Error correction of long reads
... I am posting it [here][1] since this is not answered [1]: https://bioinformatics.stackexchange.com/questions/5397/error-correction-within-the-long-read ...
written 3 months ago by IP530
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Error correction of long reads
... Hi, I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What it is done on the lab is the following: - The plasmids are purified by size - We amplify the plasmids using the phi29 polimerase. The polimerase will go trough the plasmid multiple times. Hence we get ...
nanopore pacbio sequencing written 3 months ago by IP530
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Comment: C: CIRCexplorer2 only looks for exonic circRNA
... > Is there any gene annotation file that could solve this problem? Maybe the best solution is just compare those back spliced junctions with circRNA databases and classify them as circRNA. In this case I would go for De novo indentification of circRNA: In this scenario, you scan the reads for b ...
written 3 months ago by IP530
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Comment: C: CIRCexplorer2 only looks for exonic circRNA
... Hi again :) No, CIRCexplorer2 takes two inputs: - The backspliced junctions identified by STAR ( Backspliced junction coordinates) - A gene annotation file ( file with gene coordinates) In this step, what CIRCexplorer2 does is assigning you raw signal (the backspliced read coordinates ...
written 3 months ago by IP530

Latest awards to IP

Good Answer 7 weeks ago, created an answer that was upvoted at least 5 times. For A: Predicting binding probability of circRNA and miRNA
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Scholar 3 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 3 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 4 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Popular Question 5 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 6 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Popular Question 10 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 11 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 18 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 19 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 20 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 2.1 years ago, voted at least 25 times.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 2.2 years ago, has more than 80 characters in the information field of the user's profile.

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