User: Rohit

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Rohit1.1k
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Computational biologist analyzing non-model organisms

Posts by Rohit

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Comment: C: trying to use gnu parallel and blast
... I had a problem before while using multiple IO while using blast, I thought it was a system-specific problem though :\ ...
written 2 days ago by Rohit1.1k
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Comment: C: Twobittofa download and install link?
... It's easier to download the genome from UCSC or ensembl and construct the index yourself. Also, bowtie already provides some pre-indexed [genomes][1]. If you already have the indexed files, then you can start with the alignment already. Also, 2bit format has nothing to do with the bt2 format of bowt ...
written 3 days ago by Rohit1.1k
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Comment: C: Streptococcus genome alignments
... Might it be that you are using a mapper that is tuned for illumina instead of [ion-torrent][1] data, since you did not mention the mapper you used. If you have enough coverage (~60X) then the de-novo assembly should be better if you have performed pre-processing or used an assembler that handles ion ...
written 3 days ago by Rohit1.1k
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Comment: C: trying to use gnu parallel and blast
... Isn't it with single quotes as - -outfmt '6 qseqid sseqid stitle pident length mismatch gapopen qstart qend sstart send evalue bitscore' Also, why not simply use threads as Pierre suggested? ...
written 3 days ago by Rohit1.1k
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Comment: C: Obtain all ncDNA sequences using a GTF
... What kind of non-coding sequence are you looking for? Ensembl already gives you the [ncrna][1] sequences, is there some other reason to go for the non-exonic regions again? [1]: ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/ncrna/ ...
written 6 days ago by Rohit1.1k
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Comment: C: Rescaffolding a genome assembly?
... [RACA][1] [1]: http://bioen-compbio.bioen.illinois.edu/RACA/ ...
written 6 days ago by Rohit1.1k
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Comment: C: Rescaffolding a genome assembly?
... You can probably break the contigs where there are break-points or assembly errors into fragments. Re-align the fragmented one with [medusa][1] or other scaffolders [1]: https://github.com/combogenomics/medusa ...
written 6 days ago by Rohit1.1k
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Comment: C: Need suggestions on transcriptome data
... If you have no genomic information, I think it might be hard to find the full piece of the added DNA. You can try to assemble the transcriptome denovo and map to the genome, in-order to check where you have inserts. But the problem here would be that its hard to be precise without long-read informat ...
written 6 days ago by Rohit1.1k
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Answer: A: Structural variants calling in a population
... If you are planning to look for Indels mainly, then [Freebayes][1] performs well for population data. But if you also interested in other SVs too, then you would need one of the [SV-caller pipelines][2] seperately on each of the populations and then look for those which are common in all, since call ...
written 7 days ago by Rohit1.1k
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Comment: C: Microrna Pipeline
... Can you post this as another question? Also what you need is a length filter which has nothing to do with miRNA, and has already been covered by [several][1] posts on biostar. [1]: https://www.biostars.org/p/79202/ ...
written 13 days ago by Rohit1.1k

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Popular Question 5 days ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
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Scholar 6 months ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 7 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 11 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
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Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
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Scholar 13 months ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
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Popular Question 23 months ago, created a question with more than 1,000 views. For Problem With Sam To Bam Converison After Alignment Of Scaffolds To Reference
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Popular Question 2.3 years ago, created a question with more than 1,000 views. For Compare A Denovo Assembly To The Reference Genome
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Is It A Good Idea To Trim Rna-Seq Reads Or Just Remove N'S?
Scholar 2.6 years ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Is It A Good Idea To Trim Rna-Seq Reads Or Just Remove N'S?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
Scholar 2.9 years ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs

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