User: ThePresident

gravatar for ThePresident
ThePresident140
Reputation:
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3 months, 3 weeks ago
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4 years ago
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o***************@tufts.edu

Posts by ThePresident

<prev • 76 results • page 1 of 8 • next >
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Comment: C: bwa for multiple fastq files
... Some elegant bash / awk here. +1 ...
written 18 months ago by ThePresident140
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Comment: C: Align reads on multi-fasta (contigs) file?
... What I meant by "random pairing of contigs" is that contigs probably won't be in the correct order (compared to the reference sequence), and some of them might be reversed as compared to the reference sequence i.e. the actual genome. When paired-end reads are aligned on these incorrectly joined cont ...
written 2.1 years ago by ThePresident140
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Align reads on multi-fasta (contigs) file?
... I have paired-end fastq files, however my reference genome is in a list of contigs. Thus, the referece fasta file looks something like this >contig1 AGTGCAGAC..... >contig2 GCGATCACA...... >contig3 .... Is there a way to instruct `bwa` to perform alignement on the ...
bwa written 2.1 years ago by ThePresident140
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Comment: C: How To Download All Sra Samples At Once ?
... This is brilliant! It also works for `fastq-dump`: fastq-dump --split-3 --gzip $( ...
written 2.1 years ago by ThePresident140
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... Many thanks, this looks pretty good. ...
written 2.3 years ago by ThePresident140
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... It's a good start, I can at least have the start/stop positions, the strand and nucleotide accession. One thing that would be really useful is a locus_tag. Thanks, this is still pretty good though. TP ...
written 2.3 years ago by ThePresident140
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Extracting multiple features using NCBI's e-utilities?
... I have a list of protein accession identifiers such as "CBE06962.1". I would like to automatically extract several features such as locus_tag, start and stop positions of the corresponding genes, UniProt tags etc. Is it possible to do it with by combining `esearch` and `efetch` from `e-utilities`, s ...
perl e-utilities written 2.3 years ago by ThePresident140
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Comment: C: Copy number variation using HTSeq/DESeq2
... I totally agree with all of you. I was simply curious but Kevin brought a good argument about different expected distributions in DE vs CNV. Thank you all. ...
written 2.7 years ago by ThePresident140
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Comment: C: Copy number variation using HTSeq/DESeq2
... I will, thank you for the advice. ...
written 2.7 years ago by ThePresident140
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Copy number variation using HTSeq/DESeq2
... I was wondering if the combination of HTSeq / DESeq2 (normally used for differential expression analysis in RNA-seq) could be used for copy number variation in case of DNA sequencing? I can't see why not, but again I didn't look at the math behind DESeq package. Thanks, TP ...
htseq copy number deseq written 2.7 years ago by ThePresident140 • updated 2.7 years ago by WouterDeCoster44k

Latest awards to ThePresident

Popular Question 16 months ago, created a question with more than 1,000 views. For Extract DNA sequence based on a single coordinate
Popular Question 16 months ago, created a question with more than 1,000 views. For Looking for structural variants with paired-end sequencing data
Popular Question 16 months ago, created a question with more than 1,000 views. For Bwa producing no alignment
Popular Question 16 months ago, created a question with more than 1,000 views. For Generating random DNA sequence and paired-end alignment
Popular Question 16 months ago, created a question with more than 1,000 views. For Alignment with BWA: how to discard multi mappers?
Popular Question 16 months ago, created a question with more than 1,000 views. For Extract sequence of BLAST hits
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: How To Download All Sra Samples At Once ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Copy number variation using HTSeq/DESeq2
Popular Question 17 months ago, created a question with more than 1,000 views. For Quantifying relative ratios of variants by qPCR
Popular Question 18 months ago, created a question with more than 1,000 views. For Copy number variation using HTSeq/DESeq2
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file
Popular Question 2.1 years ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Draw circular genome with selected features
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Extract sequence of BLAST hits
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Draw circular genome with selected features
Popular Question 2.3 years ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
Supporter 2.3 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file

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