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Questions tagged [sequencing]

137 questions
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Code sequence by group in R: recurring values within group

I would like to code a numerical sequence based on the combination of three columns: ID, year, and location. I want to number the years a person spent in one place as a sequence. The sequence should start anew in the year of a location change, so…
lekker
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Identifying the sequence in a recursive function

I need to identify the sequence order in the myst(n) function when it is called to then be able to give the output of myst(4). The function is defined as follow: def myst(n): if n > 1: myst(n - 1) for i in range(n): …
Charles Lamarche
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Grep that tolerates mismatches to subset .fastq

I am working with bash on a linux cluster. I am trying to extract reads from a .fastq file if they contain a match to a queried sequence. Below is an example .fastq file containing three reads. $ cat example.fastq @SRR1111111.1…
Paul
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Program error: undefined member: >>= Haskell

I'm implementing a simple interpreter in Haskell but I have this problem. The code is this: import Control.Applicative import Data.Char newtype Parser a = P (String -> [(a,String)]) parse :: Parser a -> String -> [(a,String)] parse (P p) inp = p…
Paolopast
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Error in breseq during running bowtie2

I recently tried to use breseq to analyze a few bacterial sequencing data. However, I got a fatal error when breseq used bowtie2 to align the raw data to the reference genome. Here is the critical part of the error that I got: +++ NOW PROCESSING…
Tri M. Le
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how to design SCORM package with conditional loading of next page

I am pretty new in SCORM course designing. I have a requirement to design a course as below On first page collect use input: Are you student ? If yes , load student exercise If not , load research exercise I am unable to understand how to achieve…
user269867
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How do I run this Bismark Bisulfite Sequencing program?

I am very new to coding so I'm not really sure how to approach this. I wanted to look at some data that we got and sequence them using Bismark. I already used Trim Galore to pare the reads, now I wanted to get the data into Bismark. However, I'm not…
Lost_in_Code
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Star index generation - 'std::bad_alloc' error

I was trying to generate a genome index using STAR index for mutant library 99,50 hours post fertilization (99H50) with the annotation form Lawson lab. The code I used is as follows: module load STAR; STAR --runThreadN 10 --runMode genomeGenerate…
Aranyak Goswami
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Snakemake: {input:q} does not return quoted input

I am developing an ATACseq pipeline using Genrich to run with Snakemake. The fact is that Genrich allows to call peaks from more than one replicate in the same step, avoiding additional steps (i.e. IDR). In Snakemake, I have found the way to return…
Adrià Mitjavila Ventura
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Add filename to fasta headers of multiple fasta files inside loop

I have 10 fasta files (each file with 20 gene sequences from each of the 10 samples). I would like to create 20 files, specific to each gene from 10 samples. I proceeded as follows to extract genes with the file_name in header: pyfasta extract…
bio8
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Sort and check IP address sequence

My requirements are: I have a script which takes care of finding free IPs in a given subnet (old written, works nice). I am automating to create pool of IPs, but has to be in sequence, so can be kind of wrapper for above script Execute the…
pczanwar
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Web Audio API - Scheduling Issue

I am trying to build a loop sequencer that utilises the web audio API and many different musical loops of different lengths. The general idea is that the loops are chosen at random (to a degree), then played back in in a specific order for a…
Brian Diolún
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Detection of similar sequences in ordered event lists

I have logs from a bunch (millions) of small experiments. Each log contains a list (tens to hundreds) of entries. Each entry is a timestamp and an event ID (there are several thousands of event IDs, each of may occur many times in logs): 1403973044…
Alexander Gladysh
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Modelling a sequence of operations for brewing

I'm fairly new to Haskell but I'm trying to learn a bit. I decided to write a simple homebrewing calculator as a practice project and I'm looking for some help modelling it better. My idea is that since brewing is a linear process it should be…
erik
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Implementing own sequencing in racket

I need to implement a function that takes one or more expressions and executes those expressions in order. This is what I have so far: (define (foo exp0 exp1 ) exp0 exp1)
user1025948
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