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Questions tagged [sequencing]

137 questions
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What is the idiomatic way to combine member function calls with other function calls in Scala?

Say we have an object (e.g. a list) in Scala, and we want to sequence user-defined functions with object member functions, for instance: g(l.map(f) .foldRight(...)) .map(h) If the sequence of functions is larger, the code gets a little messy.…
Matei
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Having some problem with filtering data for single cell RNA sequencing

Currently I am trying to filter some data for single cell RNA sequencing, and this process requires the use of python. I am trying to run the following codes and I am facing some errors. %pylab inline import…
Arka26
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filterAndTrim : Error in add(bin) : record does not start with '@'

I'm using dada 2 version ‘1.22.0’ on windows 10, i have list of compressed (.gz ) fastq files, when i use the function filterAndTrim i get this error message : Error in add(bin) : record does not start with '@' But when i want to see if i can read…
Reda
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Suggestions on Analyzing Protein Sequences Similarity

I want to write code to analyze short protein sequences and determine their similarity. I have no reference sequence but rather I want to write some sort of for loop to compare them all to each other to see how many duplicate sequences I have, as…
cosmomush
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SCORM course not enabling Satisfied SCO

I'm working on a course in SCORM 2004 3rd ed. and the course is not enabling the sco after it is satisfied. It allows the user to go to the next sco once it is complete but it will not enable the previous sco. It only allows the user to click the…
Jay
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Omitting NAs from Data

First time posting. Apologies if I'm not as clear as I intend. I have an excel (xlxs) spreadsheet of data; it's sequencing data if that helps. Generally indexed as follows: column 1 = organism families (hundreds of organisms down this…
KR_Tiberius
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Efficient algorithm for job sequencing, but with variable times needed

Problem: Given N tasks with potentially non-unique deadlines d1,...,dN and time needed t1,...,tN to complete each one (in hours), output a schedule that maximizes the number of deadlines met. Only 1 task can be worked on at any time. Is there an…
mega-rototo
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Animating image sequence with JavaScript

I have a sequence with images of an object from different angles. I want the object to be faux rotated when the user drags its mouse, and this I have implemented. But what I want, is when the mouse leaves the image area, that it animates the image…
rebellion
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Python pattern input recognition for CAT terminal command on Mac

I am doing RNA sequencing. I am using terminal to merge some of my fast files with a python script to do this. The python scrip has a line to determine how to recognise the files: merge: pattern_input: '(\S+)_L00\d.fastq.gz' My file names are…
Rob Staruch
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How to generate a custom bed file to use for bedtools intersect?

I have a custom reference genome, gene.fa and 18 bed files. I want to generate a bed file that contains a region of interest, 5100-5600 bp, as a single entry that I can use for intersection using bedtools intersect on my 18 bed files. I was thinking…
Cam
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Interpolate and insert missing rows into dataframe R

I am working with a large time series of oceanographic data which needs a lot of manipulation. I have several days of data missing and would like to interpolate them. Specifically date/depth/temperature. Here is an example of my df: > tibble(df) # A…
hydroceanog
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Task sequencing based on dependent tasks with parallel execution

Having a scenario where I need to identify task sequence and execute tasks possible indenpendent flows/tasks parallely. for example Task 1 Task 2 ->Task 11 and task-3 Task 3 -> Task 1 Task 4 -> Task 8 and task 12 Task 5 -> Task 9 Task 7 Task 8 ->…
Sudha Rajamanickam
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How can I convert Affymetrix probes into gene Symbols?

I have carried out Affymetrix data analysis with oligo and limma. Now I need to perform the gene enrichment analysis on the upregulated and downregulated genes (on EnrichR, by searching the gene symbols ). However, when I annotated my data (with the…
Martina M
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Binary search between two files in C

I'm trying to apply some previously written code to some DNA sequencing data that I have collected. I would like to match my sequencing reads to a document containing specific barcodes and output the number of hits for each match. I am having some…
Joe Armstrong
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Sorting dataset with abs() function

I am trying to run a gene set enrichment analysis following the vignette here: http://yulab-smu.top/clusterProfiler-book/chapter7.html I have been trying to use this particular code: data(df, package="DOSE") gene <- names(df)[abs(df) >…
Rob Staruch
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