User: IP

gravatar for IP
IP500
Reputation:
500
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
1 day, 2 hours ago
Joined:
2 years, 4 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 96 results • page 1 of 10 • next >
0
votes
4
answers
331
views
4
answers
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 4 days ago by IP500
0
votes
1
answer
125
views
1
answers
Comment: C: common CNVs among multiple files
... bedtools multiinter will help you ...
written 19 days ago by IP500
2
votes
1
answer
110
views
1
answers
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 5 weeks ago by IP500
0
votes
1
answer
110
views
1
answers
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 5 weeks ago by IP500
4
votes
1
answer
110
views
1
answer
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 5 weeks ago by IP500
1
vote
1
answer
205
views
1
answers
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 7 weeks ago by IP500
1
vote
1
answer
205
views
1
answers
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 7 weeks ago by IP500
1
vote
1
answer
205
views
1
answers
Answer: A: CIRCexplorer2 only looks for exonic circRNA
... kaixo t.blasco95! I have used CIRCexplorer2 a couple of times in the past and it did provide me information about exonic circRNA and intronic circRNA. I have check in my old outputs and that iinformation is encoded in the 14th column of the output (the one called circType). You can use the bash o ...
written 7 weeks ago by IP500
0
votes
4
answers
331
views
4
answers
Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... thanks for the corrections :) ...
written 9 weeks ago by IP500
5
votes
4
answers
331
views
4
answers
Answer: A: How to write the output in snakefile (snakemake) for bowtie2-build
... You wrote this: rule bowtie2Build: input: "refgenome/infected_consensus.fasta" output: "output/reference" shell: "bowtie2-build {input} {output}" What snakemake is going to do is to check if the file output ( in this case "output/reference" ) exist after executing the ...
written 9 weeks ago by IP500 • updated 9 weeks ago by Devon Ryan86k

Latest awards to IP

Popular Question 6 days ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Scholar 5 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 6 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 9 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Popular Question 3 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 4 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Popular Question 8 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 9 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 16 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 17 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 18 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 22 months ago, voted at least 25 times.
Scholar 2.0 years ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 2.0 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 860 users visited in the last hour