User: gbdias

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gbdias40
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Posts by gbdias

<prev • 18 results • page 1 of 2 • next >
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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 4 months ago by gbdias40
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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 4 months ago by gbdias40 • updated 4 days 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 6 months ago by gbdias40
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Thank you. This strategy worked. ...
written 6 months ago by gbdias40
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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 6 months ago by gbdias40
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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 2.2 years ago by gbdias40
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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 2.2 years ago by gbdias40 • updated 2.2 years ago by Denise - Open Targets4.6k
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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 2.4 years ago by gbdias40 • updated 2.3 years ago by Biostar ♦♦ 20
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Answer: A: Local Blast Database
... You could possibly use Bioedit. Put all files in a single one and select the "Create local protein/nucleotide database". ...
written 2.7 years ago by gbdias40
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Why Bowtie2 and Lastz give so different results?
... Hey guys, I'm mapping 50 bp reads from several ChIP-seq datasets to a short reference (170bp). I want to measure the relative enrichment of this specific consensus in the different IP conditions. It's repetitive DNA so I guess it's ok to use a consensus. To do so, I used Bowtie2 (with the --end-to ...
bowtie2 alignment chip-seq lastz written 2.7 years ago by gbdias40

Latest awards to gbdias

Scholar 4 months ago, created an answer that has been accepted. For A: Figuring out HiC restriction enzyme
Popular Question 22 months 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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