User: gbdias

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gbdias80
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Posts by gbdias

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Get chromosome sizes from fasta file
... - Another good option is to use the **faSize** command from UCSC tools. It works on any fasta file, not just UCSC genomes. - You run it like this: `faSize -detailed -tab file.fasta` - Default behavior is to print to STDOUT, so you can redirect the output to a file like this: `faSize -detailed -tab ...
written 3 months ago by gbdias80
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Answer: A: Missing or disappearing output RepeatMasker
... This is an old post but I observed the same behavior in a more recent version of RepeatMasker (4.0.7). This version already has the fix to the bug you reported above, but the behavior persists. The program apparently runs to completion and throws no error message, but the running directory is empty ...
written 4 months ago by gbdias80
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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 9 months ago by gbdias80
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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 9 months ago by gbdias80
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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 16 months ago by gbdias80
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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 16 months ago by gbdias80 • updated 12 months ago by joneill4x40
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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 18 months ago by gbdias80
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Comment: C: Extract entire reads, rather than aligned segments, from a SAM/BAM file
... Thank you. This strategy worked. ...
written 19 months ago by gbdias80
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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 19 months ago by gbdias80
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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 3.2 years ago by gbdias80

Latest awards to gbdias

Popular Question 4 months ago, created a question with more than 1,000 views. For Calculating RPKM/TPM for repetitive elements.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Figuring out HiC restriction enzyme
Popular Question 12 months ago, created a question with more than 1,000 views. For How to obtain and compare genomic coordinates from RepeatMasker output?
Popular Question 12 months ago, created a question with more than 1,000 views. For ENA/SRA updating frequency.
Scholar 16 months ago, created an answer that has been accepted. For A: Figuring out HiC restriction enzyme
Popular Question 2.9 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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