User: IP

gravatar for IP
IP350
Reputation:
350
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
20 hours ago
Joined:
1 year, 5 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 83 results • page 1 of 9 • next >
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Comment: C: How is the 2sd best hit found in bwa-mem
... ops, that was my idea, thanks :) ...
written 5 days ago by IP350
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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 days ago by IP350 • updated 5 days ago by Devon Ryan75k
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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 4 weeks ago by IP350
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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 4 weeks ago by IP350
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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 5 months ago by IP350
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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 5 months ago by IP350
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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 5 months ago by IP350
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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 5 months ago by IP350
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demultiplex a dataset when you have barcodes as a separate fastq
... Hi Biostars: I have receive raw sequencing data from a collaborator, and the data is not demultiplexed. What I usually see on the fastq files that I have to analyse and demultiplex is the following: **Barcode + sequence** And then. one can use a software like [barcode_splitter][1] or demulti ...
next-gen demultiplex sequencing written 5 months ago by IP350 • updated 5 months ago by lelle740
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Comment: C: The difference between sam files
... do you know how to code in python? P.D: Edit the original answer, this will allow others to search the question ...
written 5 months ago by IP350

Latest awards to IP

Popular Question 5 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 6 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 7 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 12 months ago, voted at least 25 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 13 months ago, has more than 80 characters in the information field of the user's profile.

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