User: ThePresident

gravatar for ThePresident
ThePresident110
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2 months, 4 weeks ago
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2 years, 10 months 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 4 months ago by ThePresident110
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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 11 months ago by ThePresident110
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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 11 months ago by ThePresident110
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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 11 months ago by ThePresident110
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... Many thanks, this looks pretty good. ...
written 14 months ago by ThePresident110
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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 14 months ago by ThePresident110
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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 14 months ago by ThePresident110
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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 18 months ago by ThePresident110
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Comment: C: Copy number variation using HTSeq/DESeq2
... I will, thank you for the advice. ...
written 18 months ago by ThePresident110
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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 18 months ago by ThePresident110 • updated 18 months ago by WouterDeCoster39k

Latest awards to ThePresident

Popular Question 4 months ago, created a question with more than 1,000 views. For Copy number variation using HTSeq/DESeq2
Popular Question 4 months ago, created a question with more than 1,000 views. For Quantifying relative ratios of variants by qPCR
Popular Question 5 months ago, created a question with more than 1,000 views. For Copy number variation using HTSeq/DESeq2
Popular Question 11 months ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file
Popular Question 11 months ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
Popular Question 11 months ago, created a question with more than 1,000 views. For Draw circular genome with selected features
Popular Question 11 months ago, created a question with more than 1,000 views. For Extract sequence of BLAST hits
Popular Question 11 months ago, created a question with more than 1,000 views. For Draw circular genome with selected features
Popular Question 14 months ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
Supporter 14 months ago, voted at least 25 times.
Popular Question 16 months ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file
Popular Question 18 months ago, created a question with more than 1,000 views. For Extract soft-clipped reads from BWA -generated SAM file

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