Stack Overflow
Stack Overflow

Questions tagged [sequencing]

137 questions
0
votes
1 answer

Using grep with patternfile returns patterns (sequence names) not in patternfile

I am cleaning up sequencing data. I have a file with reads (names) I'd like to find with grep and eventually remove. The patternfile file is 219,721 lines long, with no duplicate entries. The sequence .fastq file is 557,514,608 lines long with no…
hoytpr
  • 5
  • 3
0
votes
1 answer

Script out of bounds in R

I am using a code based on Deseq2. One of my goals is to plot a heatmap of data. heatmap.data <- counts(dds)[topGenes,] The error I am getting is Error in counts(dds)[topGenes, ]: subscript out of bounds the first few line sof my counts(dds)…
Aranyak Goswami
  • 19
  • 3
0
votes
0 answers

Fatal error: cannot open file '-c= ' : No such file or directory (SPP, phantompeakqualtools)

I am trying to run phantompeakqualtools in the terminal, I am using a WSL in Visual Studio Code. I have followed all the steps and installed dependencies to use this program as listed here: https://code.google.com/archive/p/phantompeakqualtools/ and…
Fleur Peters
  • 73
  • 6
0
votes
2 answers

Javascript functional composition/sequencing

I'm trying to understand composition and "sequencing" concept in Javascript with an exercise: Def. "composition" compose(f,g)(x) = f(g(x)) Def. "sequencing" sequence(f,g)(x) = g(f(x)) for more args sequence(f,g)(...args) = g(f(...args)) const…
zerologiko
  • 1,993
  • 1
  • 18
  • 21
0
votes
2 answers

Resequencing a column with identifier in Postgresql

The following code works and creates a temporary table with a sequence number which is restarted for every new name: with results as (select row_number() over (partition by name order BY name) as mytid,name from telephn_table) select * from results…
george
  • 1
0
votes
1 answer

Trouble Deciding How to Test for Variance in Bulk RNA sequencing Data

I have some bulk-RNA sequencing data that I need to do differential expression significance testing on. I have two conditions, WT and KO, with two replicates each, giving me a dataframe that looks like the following (the columns are in counts): …
montyman14
  • 45
  • 7
0
votes
1 answer

Stacked barplot for single cell analysis

I'm attempting to plot a stacked barplot with ggplot2 with this code barplot <- ggplot() + geom_bar(aes(y = percentage, x = TBD, fill = TBD), data = charts.data, stat="identity") I want to create a barplot for my single cell analysis that has 2…
Michelle
  • 11
  • 1
  • 4
0
votes
1 answer

How to enable kmer plot for fastQC up from v. 0.11.6

I am running fastQC on a Linux machine from the command line. Until v.0.11.5, I was used to also get a kmer plot as an output. Now, since v.0.11.6, Kmer output is disabled by default (see release notes) and I fail to find a way to enable it again. I…
Trillian Astra
  • 129
  • 1
  • 10
0
votes
0 answers

Pandas getting hung up on simple if statement

I have been trying to align sequences of DNA with pandas, but for some reason the line if mat[i][0] == mat[0][j] is taking an extremely long time to compute. It's not frozen as I can test it and see it is calculating, but it takes way too long to…
Julison
  • 11
  • 5
0
votes
0 answers

Sequential return of a string of numbers

In python, if I have a text list with names and scores I want a string of code that will reorder this list sequentially based on entry of a new or repeated name and score.
Wayne
  • 1
0
votes
1 answer

How to sequence an webserver like nodejs or kestrel in app-v?

i need to have a webserver in an app-v container. I could not find examples how to sequence and configure a webserver with app-v. Are there examples available for sequencing e.g. nodejs or even .net core webserver kestrel? Thank you for the…
Simon
  • 87
  • 5
0
votes
1 answer

How would i rename images sequentially that are within a directory structure using automator

(I have a Music Library folder - within that there are folders and subfolders - in the subfolders there are images - I need to rename these images cover.xxx cover1.xxx cover2.xxx etc and repeat for each directory. it's important to not change the…
Adam Theuma
  • 1
  • 1
0
votes
2 answers

Job sequencing with job execution time, deadlines and penalties

There is N jobs with execution times, deadlines and penalties if job misses deadline. Execution time, deadline and penalty may vary on every job. Only one job can be done at the time. And all jobs must be done. The task is to sort jobs (schedule)…
JohnnyK
  • 1
  • 2
0
votes
2 answers

GREP or AWK: Search in the first N characters of each line, and output surrounding lines that match pattern

I have a RNA-seq data that looks like this: @J00157:85:HNNJLBBXX:5:1101:2869:15047…
Ziyi Li
  • 39
  • 3
0
votes
1 answer

RNA-Seq quality control tool looking for number of aligned reads in different genomic regions

Anybody aware of a quality control tool for RNA-seq data that is checking the ratio of number of reads aligned to coding exons of genes vs number of reads aligned to introns or intergenic regions. Thanks for the help
svural
  • 961
  • 1
  • 9
  • 17
1 2 3
…
9 10