Questions tagged [genome]
for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.
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Improve a reference genome with sequencing data
I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created.
The example I ...
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How to use Python to count k-mers?
I have some FASTQ sequence files and a FASTA file for some regions I'm interested in.
I would like:
Build an index for the FASTA file
Use the index to count number of k-mers occurred in my sequence ...
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What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)
When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download?
You have a combination of choices.
First part options:
...
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How to calculate the memory usage of storing kmers in RAM
I want to write a program in C++ that stores kmers in a hash or in a trie. How can I calculate how much RAM I would need for each type of data structure? For this application my kmers are strand-...
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How do PCR duplicates arise and why is it important to remove them for NGS analysis?
I am trying to understand PCR duplicates in NGS analyses (actually whole-genome). I searched, and the best answer I found is in this blog.
However I don't understand if I understood how PCR ...
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How can I locate duplicated regions in a sequence?
I am facing an issue when trying to align short reads against a region in human chr5. The two Sensory Motor Neuron genes, (SMN1 and SMN2) are almost 100% identical and this causes the aligner to fail ...
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What is the file .mums created by mummer?
I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are:
1.create a file .mums with the following command line:
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Samtools Index: Chromosome Blocks not Continuous
I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
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Use of Electronic Phenotype in EHR
May I know what's the use of Electronic Phenotyping using EHR data?
I did refer this link but have few questions
I understand that ...
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Create BED file from list with gene symbols
Is there a way to generate a BED file of a list of gene symbols for a given genome?
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