User: Fred

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Fred710
Reputation:
710
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Trusted
Location:
Paris, France
Website:
http://twitter.com/fre...
Last seen:
1 year, 9 months ago
Joined:
9 years, 2 months ago
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Posts by Fred

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... About the dry run option, if I am not wrong, nextflow does not have it because it does not know a priori what will be the exact execution dag. Nextflow language is more expressive and the execution dag may depends on the input data if you have conditional executions in your workflow for example (whi ...
written 23 months ago by Fred710
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Answer: A: fasta as input file : mapping sequences to a genome
... gmap indeed allows you to align sequences in FASTA with a reference genome. It can output alignments in SAM format: # Build reference genome database gmap_build -D dir/ -d refgenome dir/refgenome.fa # Alignment gmap -D dir -d yourgenome -f samse -t 8 yourfasta.fa | samtools view -Shb - | samtools ...
written 4.7 years ago by Fred710
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Answer: A: Downsampling dataset with more than 60 million reads
... Maybe something like that could help: #!/usr/bin/perl use strict; use warnings; # # Usage ./sampleFastq.pl <fastq r1> <fastq r2> <outFastq r1> <outFastq r2> <prob of keeping reads> # open(FASTQF,$ARGV[0]); open(FASTQR,$ARGV[1]); open(FASTQOUTF,">".$ARGV[2]); open(F ...
written 4.7 years ago by Fred710
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Answer: A: CNV analysis tool on exome data for NGS
... Maybe you can try "Control FREEC", that handles exome sequencing data. http://bioinfo-out.curie.fr/projects/freec/   ...
written 5.1 years ago by Fred710
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Answer: A: Count The Number Of A, T, G And C At Specific Genomic Locations For Multiple Rna
... I once found this tool: pileup2base that outputs the number of A C G T and INDELs for each positions of a mpileup file. Maybe you can test it. If you want to generate the mpileup for a particulat position you can do: samtools view -h indexed_bam_file.bam chr:start-end | samtools view -Shb - | samt ...
written 5.2 years ago by Fred710
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Comment: C: Problem In Cuffdiff Output
... Your gtf file seems to be automatically generated by a gene prediction program. So it does not contain any gene annotation (such as gene name, gene id, etc. ) ...
written 5.5 years ago by Fred710
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Answer: A: Problem In Cuffdiff Output
... It seems that you don't use a reference GFF/GTF file containing known transcripts and gene names. You should use a gff/gtf file ( for example the genes.gtf file in one of the archives here http://tophat.cbcb.umd.edu/igenomes.shtml ) in the cuffcompare step: cuffcompare -r genes.gtf <input1.gtf ...
written 5.5 years ago by Fred710
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Answer: A: The Organisation Of Really Contrived Acronyms (Orca)
... I Just found this one: PARSEC: PAtteRn SEarch and Contextualization ...
written 5.7 years ago by Fred710
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Comment: C: Mirna Expression Based On Tissue
... Otherwise, there is this article, published in Genome Research this year, in which you can find miRNA expression in different organs (cerebellum, brain, testis, heart, kidney) for 6 species. The normalized counts are provided as supplemental material. ...
written 5.7 years ago by Fred710
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Answer: A: Mirna Expression Based On Tissue
... Did you look at microrna.org ? It has been published in 2007 in NAR. The expression data (from 2008) can be downloaded from the website. ...
written 5.7 years ago by Fred710

Latest awards to Fred

Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Way To Run Bedtools In Parallel With Blocking
Supporter 5.1 years ago, voted at least 25 times.
Voter 5.1 years ago, voted more than 100 times.
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Problem With Ucsc Liftover Tool
Good Answer 6.3 years ago, created an answer that was upvoted at least 5 times. For A: What Is The Best Way To Run Bedtools In Parallel With Blocking
Appreciated 6.3 years ago, created a post with more than 5 votes. For A: What Is The Best Way To Run Bedtools In Parallel With Blocking
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Way To Run Bedtools In Parallel With Blocking
Teacher 6.4 years ago, created an answer with at least 3 up-votes. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Appreciated 6.4 years ago, created a post with more than 5 votes. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Good Answer 6.4 years ago, created an answer that was upvoted at least 5 times. For A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
Appreciated 7.8 years ago, created a post with more than 5 votes. For A: Extract User Defined Region From An Fasta File
Good Answer 7.8 years ago, created an answer that was upvoted at least 5 times. For A: Extract User Defined Region From An Fasta File
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