User: IP

gravatar for IP
IP550
Reputation:
550
Status:
Trusted
Location:
Denmark/University of Copenagen
Last seen:
6 hours ago
Joined:
2 years, 10 months ago
Email:
p*******@hotmail.es

Posts by IP

<prev • 103 results • page 1 of 11 • next >
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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 19 days ago by IP550
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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 19 days ago by IP550
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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 7 weeks ago by IP550
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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 7 weeks ago by IP550 • updated 7 weeks ago by WouterDeCoster39k
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Comment: C: Insert mutations in a reference genome from a vcf
... I have test this tool, and it is doing (ultrafastly!) what I was looking for. Thanks! ...
written 4 months ago by IP550
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Insert mutations in a reference genome from a vcf
... Hi Biostars, I am looking for a tool to introduce variants in a reference genome. **The ideal tool I am looking for:** *Takes as input:* - genome fasta - a vcf file *What it does:* - Insert some of the variants (randomly) present in the vcf into the reference genome *What is the output* ...
simulation snp sequencing written 4 months ago by IP550 • updated 4 months ago by WouterDeCoster39k
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Comment: C: Differential expression: replicates in one condition, no replicates in the other
... Hi, thanks for the answer! that was actually what I finished doing. I had a 4 biological replicates for the "healthy" group and think that things worked fine cheers, ...
written 4 months ago by IP550
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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 6 months ago by IP550
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Comment: C: common CNVs among multiple files
... bedtools multiinter will help you ...
written 6 months ago by IP550
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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 7 months ago by IP550

Latest awards to IP

Centurion 7 weeks ago, created 100 posts.
Scholar 7 weeks ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Predicting binding probability of circRNA and miRNA
Popular Question 6 months ago, created a question with more than 1,000 views. For Get the 5'UTR of a set of genes
Scholar 7 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 7 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Appreciated 8 months ago, created a post with more than 5 votes. For A: How to write the output in snakefile (snakemake) for bowtie2-build
Scholar 8 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
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 10 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Popular Question 14 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 15 months ago, created a question with more than 1,000 views. For fastqc overrepresented sequences
Popular Question 22 months ago, created a question with more than 1,000 views. For Programs of UCSC utilites
Scholar 23 months ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Scholar 2.0 years ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Pysam changes bam format when printing
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Tophat vs Tophat-fusion concordant alignment rate
Autobiographer 2.5 years ago, has more than 80 characters in the information field of the user's profile.

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