User: Rohit

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Rohit1.3k
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Computational biologist analyzing non-model organisms

Posts by Rohit

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Comment: C: Tool to do Variant calling from contigs data
... Variant calling without much effort can be done with [Freebayes][1] although you need to filter for false positive calls(vcffilter step). However, as a start, it is best to go through the [best practices][2] offered by GATK since pre-processing makes a huge difference. [1]: https://github.com/ek ...
written 5 months ago by Rohit1.3k
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Comment: C: How to use pacbio reads to join contigs
... Do you have enough coverage i.e. 10X for pacbio. Since DBG2OLC requires multiple alignment of the pacbio reads, if there is lower coverage, It might be easier to clarify if you provide the actual command used, since it doesn't help you have a higher kmer_coverage threshold and low sequencing coverag ...
written 7 months ago by Rohit1.3k
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Comment: C: short RNA reads alignment
... [Segemehl][1] is also a good option, since you can specify the minimum length of the spliced fragment (-Z option) in your case and also increase the accuracy (-A) and decrease evalues for split alignments (-w). [1]: http://www.bioinf.uni-leipzig.de/Software/segemehl/ ...
written 8 months ago by Rohit1.3k
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Comment: C: Variant calling in genomic chunks
... If you plan on calling SNPs only then I don't see a problem. However, if you are looking for structural variants, there would be missing data on the edges of the chunks, especially for SVs spanning multiple chunks. Additionally, how do you plan to keep track of the size or exact position, additional ...
written 8 months ago by Rohit1.3k
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Comment: C: Judging best assembly
... This is the best option, multiple assemblers and multiple kmers. Decreasing the coverage cut-off for contiguity doesn't help as it increases changes of erroneous overlaps. ...
written 8 months ago by Rohit1.3k
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Comment: C: k-mer optimization in Trinity
... It definitely is advisable, but not sure if possible. At least the earlier versions of trinity (2-3 years ago) had fixed kmer sizes in chrysalis step (clustering), but other steps can use a user-defined kmer. Additionally, there was an upper bound of 32 for kmer length. ...
written 8 months ago by Rohit1.3k
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Answer: A: Judging best assembly
... [Contig-ordering tools][1] can help in orientation with the help of reference. However, only the contiguity of the genomes with N50, NNG50, L50, LG50 do not mean that the assembly is best. The quality of the assembly matters too, which are compared using CEGMA or BUSCO metrics. In the end, it all ma ...
written 8 months ago by Rohit1.3k
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Answer: A: Help with finding gene families in genome
... [Omicstools][1] is a good source for suggestions. If you have the amino acid sequences, interproscan does a great job in annotation. If you are looking into TMM or signal peptides in particular, [signalP][2] or [TMHMM][3] are useful. [Trinotate][4] is another annotation pipeline setup for *de novo* ...
written 8 months ago by Rohit1.3k
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Comment: C: How to combine multiple tools to detct SVs in WES data
... NextSV is based on long-reads, I don't think you can apply it your data. [IntanSV][1] seems good, never tested it though. [1]: https://bioconductor.org/packages/release/bioc/html/intansv.html ...
written 9 months ago by Rohit1.3k
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Answer: A: How to combine multiple tools to detct SVs in WES data
... [SV-Merge][1] and [MetaSV][2] already perform merging with illumina-paired end data. If you have long-reads, then give [NextSV][3] a try. [1]: http://svmerge.sourceforge.net/ [2]: https://github.com/bioinform/metasv [3]: https://github.com/Nextomics/nextsv ...
written 9 months ago by Rohit1.3k

Latest awards to Rohit

Appreciated 14 months ago, created a post with more than 5 votes. For A: Fastqc Over-Represented Sequences Are Adapters ?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Fastqc Over-Represented Sequences Are Adapters ?
Great Question 14 months ago, created a question with more than 5,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Scholar 16 months ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: RNA seq assembly and CEGMA
Popular Question 18 months ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 19 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 2.0 years ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Kmer Frequency Distribution And Genome Complexity
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Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Introducing Reputation Threshold For Creating New Tags.
Scholar 2.6 years ago, created an answer that has been accepted. For A: How do denovo genome/transcriptome assemblers treat ambiguous bases?
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Great Question 3.0 years ago, created a question with more than 5,000 views. For Best Hits From Blast Tabular Output Of Multiple-Queries
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Popular Question 3.4 years 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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