User: shwethacm

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shwethacm200
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Seattle, WA
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Posts by shwethacm

<prev • 25 results • page 1 of 3 • next >
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Answer: A: Assembly of wheat genome
... 1. Do the usual : N50, assemblathon like calculations 2. BUSCO for evaluating completeness of gene models (+1 to @h.mon) 3. Align against current reference : for the contigs that do not align, are they misassemblies or collapsed duplications or proper assembled parts that the current reference faile ...
written 16 months ago by shwethacm200
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Answer: A: Custom extract reads from a sam/bam file into a valid sam/bam
... Gotcha! I realized that the mistake I was making was in appending the header separately in the end, which resulted in an ad-hoc mush of a samfile. Your method is so much more elegant! Thanks, Pierre! ...
written 23 months ago by shwethacm200
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Custom extract reads from a sam/bam file into a valid sam/bam
... Hi there, I am trying to "brute-force" split a bam file using grep. The reason why I am doing this is because I am trying to split by a custom tag that looks like these (bc would be the tag): bc:B:S,1,1 bc:B:S,0,0 bc:B:S,2,2 (( But I cannot used bamtools because "bc" is not a recognized tag ...
genome next-gen alignment written 23 months ago by shwethacm200
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Answer: A: Criteria for filtering contigs after spades assembly
... Why don't you map your input reads back to the assembly and calculate the mean depth ? 2 std deviations from the mean could be your cutoff! ...
written 23 months ago by shwethacm200
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Comment: C: Next step after the assembling
... While I do not have the experience to advice you about the IS issue, I can suggest some standard general checks for you scaffolds: 1. Yes, adapters often linger and make their way into the assembly contigs sometimes. You can use NCBI's contamination detection pipeline to identify these. Which brin ...
written 2.4 years ago by shwethacm200
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Answer: A: Scaffolding with pacbio reads
... If you already have contigs, then you can put them into scaffolds using many tools. Re-assembly along with PE data is not necessary - you will not be gaining anything! Here's a paper that outlines many PE scaffolding tools: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r42 ( ...
written 2.4 years ago by shwethacm200
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Comment: C: Nominal length vs insert size
... At this point, I am confused about what your end goal is. So far, it seemed like you wanted to figure out the insert size of your PE reads, right ? You can use any alignment program to map, so long as you map it to the right reference, and have a sam/bam file in the end, you can find out the insert ...
written 2.4 years ago by shwethacm200
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Answer: A: Scaffolding with pacbio reads
... Hi guillaume.rbt, If you are looking to reuse your PacBio reads for scaffolding, that is pretty much a dead end. If you are asking your question because you do not want to sequence a separate PE library, then you could look to see if there short-read based assemblies and PE libraries for the sam ...
written 2.4 years ago by shwethacm200
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Comment: C: Nominal length vs insert size
... Hi Nusrat, About references: Technically, you cannot use "any" sequence as a reference. What is the source (species) of your sequencing reads? If it is human, you can map it to the latest human assembly (hg38) to calculate insert size. In general, if you have an assembly for the species you sequ ...
written 2.4 years ago by shwethacm200
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Answer: A: Downloading genomic interval for hg38
... UCSC table browser has what you need (and more! ) https://genome.ucsc.edu/cgi-bin/hgTables (( PS: CpG information is under group:Regulation )) ...
written 2.4 years ago by shwethacm200

Latest awards to shwethacm

Popular Question 16 months ago, created a question with more than 1,000 views. For BLASR: How to subsample alignments from a region
Scholar 16 months ago, created an answer that has been accepted. For A: Assemble genomes over 100 Mb with the portal SMRT Analysis Software v4.0
Appreciated 17 months ago, created a post with more than 5 votes. For A: Scaffolding with pacbio reads
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Polymorphic and 'highly' heterozygous
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Scaffolding with pacbio reads
Scholar 2.4 years ago, created an answer that has been accepted. For A: Assemble genomes over 100 Mb with the portal SMRT Analysis Software v4.0
Supporter 2.4 years ago, voted at least 25 times.
Scholar 2.4 years ago, created an answer that has been accepted. For A: Assemble genomes over 100 Mb with the portal SMRT Analysis Software v4.0
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Bed file: merging intervals that overlap a certain percentage

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