User: IP

gravatar for IP
IP620
Reputation:
620
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
11 minutes ago
Joined:
3 years, 5 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 109 results • page 1 of 11 • next >
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Comment: C: Useful productivity tools for bioinformaticians
... I label my bioinformatics calendar as "before Snakemake" and "after Snakemake" ...
written 4 weeks ago by IP620
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Annotation of structural variant mechanism
... Hi biostars, I have detected a set of deletions in my samples, and now I want to classify the deletions into a DNA repair pathway such as Non Homologous End Joining or Homologous Recombination. I have seen that there are some tools out there (e.g. [BreakSeq2][1]) but I have not found any evaluatio ...
annotation structural-variation sequencing written 7 weeks ago by IP620
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Comment: C: How to extract the circRNA sequences based on the the back-spliced junctions det
... Hi Davide, I have no idea. I encourage you to create a new post with that ...
written 11 weeks ago by IP620
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Comment: C: Problem in setting pipeline for circDNA prediction analysis.
... Dear Abdul, Regarding the error with the python installation, probably you have a python version lower than 3.0. Circle-Map is implemented on python 3.6 and I do not plan to support versions of python lower than that. I have update the github readme accordingly. Sorry for the confusion. What is the ...
written 6 months ago by IP620
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Comment: C: Circle-Map: Sensitive detection of circular DNA at single-nucleotide resolution
... I have post an answer in [the other thread][1] [1]: https://www.biostars.org/p/347488/#382429 ...
written 6 months ago by IP620
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Answer: A: Problem in setting pipeline for circDNA prediction analysis.
... Dear Abdul, Thanks for using Circle-Map. The reason you are getting the error is because your system is using bash and not python to interpret the code. And of course, bash does not understand python. I think that this error was caused because the source code was directly downloaded from github i ...
written 6 months ago by IP620
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Tool: Circle-Map: Sensitive detection of circular DNA at single-nucleotide resolution using guided realignment of partially aligned reads
... Circle-Map is an easy to install, python package that implements all the steps required to detect extrachromosomal DNA circles. Circular DNA (also called eccDNA,ecDNA,circDNA...) have recently gained quite attention due to their role in cancer as a mutational process in eukaryotic genomes.The packag ...
ecdna circdna tool eccdna written 7 months ago by IP620
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Answer: A: Problem in setting pipeline for circDNA prediction analysis.
... Dear Abdul, We have publish today on biorvix a preprint with a new algorithm for circular DNA detection. https://www.biorxiv.org/content/10.1101/654194v1 The code is now publicly available via github (https://github.com/iprada/Circle-Map) and it contains a step-by-step tutorial (https://github.co ...
written 7 months ago by IP620
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Comment: C: Infer order of supplementary alignments [pysam]
... Looks cool! I just had a quick look at the code and it seems that it is a better approach for high throughput processing of the nanopore complex reads. Thanks a lot for sharing! ...
written 8 months ago by IP620
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Answer: A: Infer order of supplementary alignments [pysam]
... Hi, We (in our lab) had a similar problem, were we have reads with many supplementary alignments. Apparently, more people has the same problem as [you and me][1] In order to get the supplementary tag as a function of the query (read), what I did was the following: 1. Align the reads with minimap ...
written 8 months ago by IP620 • updated 8 months ago by WouterDeCoster42k

Latest awards to IP

Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Useful productivity tools for bioinformaticians
Great Question 5 weeks ago, created a question with more than 5,000 views. For Programs of UCSC utilites
Great Question 6 weeks ago, created a question with more than 5,000 views. For Programs of UCSC utilites
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Scholar 6 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Centurion 8 months ago, created 100 posts.
Scholar 8 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Popular Question 9 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 9 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Predicting binding probability of circRNA and miRNA
Popular Question 13 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Scholar 14 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 14 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 14 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 15 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 15 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Popular Question 16 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 17 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Popular Question 21 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 23 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 2.5 years ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing

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