User: gbdias

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gbdias60
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Posts by gbdias

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Comment: C: How to visualize duplicated segments in a de novo Whole Genome Assembly
... Hi, Sorry if the question was not clear. I guess a simpler way to phrase it would be: How do you align a full diploid assembly to a haploid reference genome and visualize it in dot plot style. Thanks for the D-Genies suggestion. I suspect it will do the same as MUMmerplot but I will take a look. ...
written 19 hours ago by gbdias60
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How to visualize duplicated segments in a de novo Whole Genome Assembly
... Hi, I am searching for tools to visualize regions of a whole genome assembly that are represented twice or more times. - Most genome assemblers will collapse haplotypes that are similar enough, generating a "pseudo-haploid" final assembly. - However, if the haplotypes are divergent past a certain ...
wgs visualization duplication written 1 day ago by gbdias60
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Answer: A: Figuring out HiC restriction enzyme
... Figured it out by checking the overrepresented k-mers at the FASTQC report for my data. ...
written 7 months ago by gbdias60
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Figuring out HiC restriction enzyme
... Hi, Does anyone have a strategy for figuring out which restriction enzyme was utilized in a HiC experiment based on the Illumina reads alone? Thanks ...
hi-c hic scaffolding written 7 months ago by gbdias60 • updated 3 months ago by joneill4x30
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... An alternative I found is to use [seqtk][1]. It takes a list of sequence names in a file and extract the sequences from FASTA/Q. seqtk subseq in.fq name.lst > out.fq [1]: https://github.com/lh3/seqtk/ ...
written 9 months ago by gbdias60
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Thank you. This strategy worked. ...
written 9 months ago by gbdias60
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Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Hello, I am trying to extract long reads from the Blasr .sam output. However, I want to collect the **entire** raw reads that produced alignments, and not just the aligned segments. Is there an easy way to do this? Here is the blasr command I am using: blasr -noSplitSubreads -clipping none ...
bam sam blasr written 9 months ago by gbdias60
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Comment: C: What's the difference between WGS and RefSeq databases?
... Thank you for the explanation. What if I wanted to find all ERVs in a primate genome, for example. Knowing that most of these sequences are not annotated, the WGS is the option to go, right? I mean, the Refseq would not include non-annotated non-protein-coding sequences even if they are assembled in ...
written 2.5 years ago by gbdias60
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What's the difference between WGS and RefSeq databases?
... I read the Refseq documentation in the NCBI handbook but it is still not clear to me. I'm aware WGS represents all assembled contigs from a sequencing project, and Refseq supposedly has some curation... Does that mean WGS is more complete than Refseq (even if it includes a bunch of unnannotated fea ...
ncbi wgs refseq written 2.5 years ago by gbdias60 • updated 2.5 years ago by Denise - Open Targets4.7k
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Calculating RPKM/TPM for repetitive elements.
... Hey guys, The RPKM and TPM measures correct for read depth and gene lenght, and work reasonably well when dealing with single copy genes. However, what if I want to mapp transcripts to a repetitive element (e.g. transposon)? How do I calculate transcript abundance in a way that I'm able to compare ...
rpkm tpm rna-seq written 2.7 years ago by gbdias60 • updated 2.5 years ago by Biostar ♦♦ 20

Latest awards to gbdias

Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Figuring out HiC restriction enzyme
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to obtain and compare genomic coordinates from RepeatMasker output?
Popular Question 3 months ago, created a question with more than 1,000 views. For ENA/SRA updating frequency.
Scholar 7 months ago, created an answer that has been accepted. For A: Figuring out HiC restriction enzyme
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How can I deal with adapter contamination in next-gen sequencing reads?

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