User: Rohit

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Rohit1.2k
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Computational biologist analyzing non-model organisms

Posts by Rohit

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Comment: C: How can I right align InDels ?
... Is there a particular reason that last of the A in the homopolymer is pushed in the middle of the indel and the indels are not clustered together? I might be naive, wouldn't the moving of the indels remove all the sense from the alignment. I wouldn't change the alignments without looking into the r ...
written 4 weeks ago by Rohit1.2k
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Comment: C: Assembling PacBio reads using a reference genome
... I personally do not know any reference guided pacbio assemblers. You can 1) Map the reads to the reference, go for local assemblies and then scaffold based on the complete set of pacbio reads 2) de novo assemble everything, then scaffold using the reference The 2nd option is better since if ther ...
written 4 weeks ago by Rohit1.2k
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Answer: C: empty SAM file
... Isn't the command `bowtie -m 1 -S bowtie_index/mm10 Oct4.fastq Oct4.sam` You don't need a directed output ">" ...
written 4 weeks ago by Rohit1.2k
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Comment: C: Closest gene to set of intervals
... You would need a bed file of [gene boundaries][1] for this [1]: ftp://ftp.ensembl.org/pub/release-89/gff3/homo_sapiens ...
written 7 weeks ago by Rohit1.2k
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Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
... I agree, this would destroy the original file - horrible experiences with sed -i and grep > (instead of grep '>') ...
written 7 weeks ago by Rohit1.2k
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Comment: C: LASTZ does not accept/like "-" (dash) in Fasta file
... You can use sed to replace the file first, `sed -e '/^[agctn]/ s/-/n/g' file1.fa >file2.fa` Additionally you have to use the --ambiguous=n and query.fa[unmask] options since you have lower-case letters. ...
written 7 weeks ago by Rohit1.2k
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Answer: A: Closest gene to set of intervals
... I am not sure if you have tried, bedtools [closest][1] already does everything (apart from name extraction) what you need. You can use the -D or -d options with -ref (with respect to reference) to check which is the closest with/without direction involved. [1]: http://bedtools.readthedocs.io/en/ ...
written 7 weeks ago by Rohit1.2k
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Comment: C: Help with finding introns
... Intron needs to be defined according to the gene boundary the cdna falls in, so you would need the gene boundary along with the cdna coordinates ...
written 7 weeks ago by Rohit1.2k
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Comment: C: Help with finding introns
... You might not be able to get the intron sequences from a fasta file with only cDNA. You need a bed/gff [file][1] with gene boundaries for the cDNA you are interested in and then you extract the regions that [are not][2] cDNA. Just keep in mind that your gene boundaries need to start and end with the ...
written 7 weeks ago by Rohit1.2k
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Comment: C: Gene lists and calculated Ka/Ks ratio per gene
... Since Ka/Ks ratios are compared to for a reference species with respect to another, which species do you want to compare it to? Ensembl has the calculated dN/dS in their ortholog comparison for each of the genes searched, also ensembl biomart has the calculated dN and dS (seperately) for the ortholo ...
written 7 weeks ago by Rohit1.2k

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
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Teacher 9 months 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 3.0 years ago, created an answer that has been accepted. For A: De Novo Genome Assembler Preferring Shorter Error-Free Contigs

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