User: IP

gravatar for IP
IP360
Reputation:
360
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
6 days, 20 hours ago
Joined:
1 year, 11 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 85 results • page 1 of 9 • next >
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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 10 weeks ago by IP360
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Comment: C: 4C interaction analysis
... 4Cker gave me some good results a year ago ...
written 10 weeks ago by IP360
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Comment: C: How is the 2sd best hit found in bwa-mem
... ops, that was my idea, thanks :) ...
written 5 months ago by IP360
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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 5 months ago by IP360 • updated 4 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 6 months ago by IP360
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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 6 months ago by IP360
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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 11 months ago by IP360
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Differential expression: replicates in one condition, no replicates in the other
... Hi Biostars: I am facing a problem with differential expression analysis, were due to the intrinsic features of the samples we can't have replicates in one condition. **Study design:** We have a patient with a very rare translocation , no other similar translocation has been described in the worl ...
rna-seq edger sequencing written 11 months ago by IP360
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Comment: C: demultiplex a dataset when you have barcodes as a separate fastq
... If that is the answer, I assume that they have done something wrong, this is not a standard format for providing the data, right? Whatever your answer is, thanks for repplying ...
written 11 months ago by IP360
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Comment: C: The difference between sam files
... You can achieve speed by sorting the bam files by query name, then, you can loop trough both files ...
written 11 months ago by IP360

Latest awards to IP

Popular Question 3 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 4 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 Programs of UCSC utilites
Scholar 12 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 13 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 17 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

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