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Questions tagged [sequencing]

137 questions
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Sequencing documents in distributed CouchDB system

I am implementing a distributed audio repository on which registered users can create audio recordings and share these with other registered users. Ideally we would like to run the repository on a few (n<5) laptops that are intermittently connected…
Thomas
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Scrapy forum scraping, synchronization strategies between the item pipeline and the request processors

Dissclaimer This question is hard to answer directly, and you will need to have a good understanding of scrapy and program sequencing to answer it. It is hard for me to shrink wrap the question into something easier to directly answer. AFAIK one…
Hassan Syed
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Samtools mpileup : error reading from input file

I am writing a code to analyse yeast sequencing data using R. I was able to do the alignment using BWA and thus obtain a .bam file and its .bai index using samtools. My next step is to perform variant calling using bcftools. Here is my command line…
Juliette G.
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Segmentation fault on an old software loading fasta?

I'm fairly new to c++ but I'm trying to learn. I've been tasked with implementing an old software called snpomatic in our pipelines. I could successfully build the program and run it with some datasets (i.e. a genome in fasta format and sequencing…
JLR
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Pheatmap Annotation Row

Excuse Essay So I’ve done a Deseq analysis, then taken the counts file, applied the same names and then removed an NA values , then created a ?tibble/table called sigs, which I then turn into a Data frame: sigs <- na.omit(res) sigs Looks something…
Rob Staruch
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Find sequencing reads with insertions longer than number

I'm trying to isolate, from a bam file, those sequencing reads that have insertions longer than number (let's say 50bp). I guess I can do that using the cigar but I don't know any easy way to parse it and keep only the reads that I want. This is…
PaulaO
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Why might the Scheme `filter` form not process list elements 'in order'?

(filter procedure list) applies procedure to each element of list and returns a new list containing only the elements for which procedure returns true. (R. Kent Dybvig The Scheme Programming Language) (online) What may not be apparent from this…
mnemenaut
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STAR mapping is creating empty BAM file

I'm trying to run STAR but I am getting an empty BAM file. Does anyone know why this is happening and how to fix it? iCount mapstar demultiplexed/demux_NNNGGCGNN.fastq.gz hs88 mapping_NNNGGCGNN \ > --annotation homo_sapiens.88.gtf.gz #for context,…
user12006540
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set a sequence on a list of items

I need to set up a recursive function in C# to set the sequence number of a list of items. More specifically a bom. For each bom level, I need to start the sequence at 10, and increment of 10. How do I keep track of what level i'm at, and what…
André Cooke
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Can analysis of GWAS/WES/WGS be performed with DNA from saliva in combination with DNA from blood?

Can statistical analyses (GWAS/WES/WGS) be performed with DNA from saliva in combination with DNA from blood? Is there a chance of bias? First, I think DNA=DNA, in other words, no matter how the 'DNA code' is collected. But there may be unexpected…
P.Roberto Bakker ev Doornebal
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haskell *> sequencing operator

I have a question arising from the answer to my question at: haskell Either and Validation Applicative My code is posted there. It concerns the use of the *> sequencing operator instead of the <*> applicative operator. Based on the explanation at…
maxloo
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R: Get index of first instance in vector greater than variable but for whole colum

I am trying to create a new variable in a data.table. It is intended to take a variable in the data.table and for each observation compare that variable to a vector and return the index of the first observation in the vector that is greater than the…
JotHa
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Scheduling Audio Sample Playback on iOS

In an iOS app (Swift), how would I schedule audio samples to playback at exact times? I'd like to make music by scheduling audio samples to play at exact times - a series of "tracks". I have some idea that I should be using AVFoundation, but I find…
John McDowall
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How to count characters across strings in a pandas column

I have a dataframe with the following structure: prod_sec A AA AAAAAAAAAAB AAAABCCCAA AACC ABCCCBAC df = pd.DataFrame({'prod_sec': ['A','AA','AAAAAAAAAAB','AAAABCCCAA','AACC','ABCCCBAC']}) Each string is a sequence made up…
Jonathan Hay
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Vcf to Bayescan format - perl script not recognising populations

I am trying to convert a .vcf file into the correct format for BayeScan. I have tried using PGDSpider as recommended but my .vcf file is too big so I get a memory issue. I then found a perl script on Github that may be able to convert my file even…
QPaps
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