User: ThePresident

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ThePresident90
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Posts by ThePresident

<prev • 75 results • page 1 of 8 • next >
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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 9 days ago by ThePresident90
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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 10 days ago by ThePresident90
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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 25 days ago by ThePresident90
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Comment: C: Extracting multiple features using NCBI's e-utilities?
... Many thanks, this looks pretty good. ...
written 3 months ago by ThePresident90
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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 3 months ago by ThePresident90
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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 3 months ago by ThePresident90
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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 7 months ago by ThePresident90
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Comment: C: Copy number variation using HTSeq/DESeq2
... I will, thank you for the advice. ...
written 7 months ago by ThePresident90
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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 7 months ago by ThePresident90 • updated 7 months ago by WouterDeCoster30k
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Comment: C: DAVID not accepting locus_tag identifiers. Alternatives?
... Thank you Kevin, I really appreciate the effort. One thing I didn't mention is that I have or rather know all bacterial species associated with the locus_tag's. The problem is that some of them contain more relevant info (such as GeneID or "old locus_tag" that is sometimes recognized by DAVID), but ...
written 9 months ago by ThePresident90

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Popular Question 25 days ago, created a question with more than 1,000 views. For Draw circular genome with selected features
Popular Question 3 months ago, created a question with more than 1,000 views. For bowtie --fr/--rf/--ff reporting
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Popular Question 5 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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