User: IP

gravatar for IP
IP430
Reputation:
430
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
14 hours ago
Joined:
2 years, 2 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 88 results • page 1 of 9 • next >
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... thanks for the corrections :) ...
written 4 days ago by IP430
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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 6 days ago by IP430 • updated 6 days ago by Devon Ryan85k
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Answer: A: circRNA-Seq analysis tools
... Hi! **To answer your questions:** There are plenty of tools to detect circRNAs from RNA-Seq data such as CIRCexplorer2 or just using STAR alignment with chimeric reads option but do they still apply to circRNA-Seq in my case? tools like CIRCexplorer2 definitively work for circRNA enriched RNA- ...
written 6 weeks ago by IP430
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Answer: A: 4C interaction analysis
... 4Cker gave me some good results a year ago. And you can still get some contact maps when you do not have replicates. What I remember is that if your data quality standards are not good ([See section 5.2][1]), 4Cker will produce really wrong results. So I suggest: 1- Make sure that your data is good ...
written 5 months ago by IP430
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Comment: C: 4C interaction analysis
... 4Cker gave me some good results a year ago ...
written 5 months ago by IP430
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Comment: C: How is the 2sd best hit found in bwa-mem
... ops, that was my idea, thanks :) ...
written 9 months ago by IP430
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How is the 2nd best hit found in bwa-mem
... Hi biostars! I have a question about how is the 2nd best hit found in bwa-mem for calculating the mapping quality. From the [bwa paper][1], it is stated that the mapping quality scores are calculated using a similar algorithm as in the [MAQ][2] aligner. In the MAQ paper one can found the following ...
bwa-mem written 9 months ago by IP430 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: How to extract the circRNA sequences based on the the back-spliced junctions det
... Then, you can use pysam module,example: import pysam as ps genome_fa = '/path/to/genome/fasta' fastafile = ps.FastaFile(genome_fa) sequence = fastafile.fetch(chr1,100, 200) Of course, then you can get the complementary if it is the minus strand using biopython or coding by scr ...
written 10 months ago by IP430
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Comment: C: How to extract the circRNA sequences based on the the back-spliced junctions det
... do you know how to program in python or use bash? ...
written 10 months ago by IP430
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Comment: C: To screen for a good aligner
... Which kind of sequencing data are you working? I am wondering why you want to do this ...
written 14 months ago by IP430

Latest awards to IP

Appreciated 5 days ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 5 days ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Popular Question 6 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 7 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 14 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 15 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 16 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 20 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 22 months ago, has more than 80 characters in the information field of the user's profile.

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