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Questions tagged [sequencing]

137 questions
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Oracle - User defined sequencing issue

Explanation: There are 2 tasks A & B which are scheduled daily & monthly respectively. Nature of Tasks: All the tasks have a seq_number assigned to it which is unique. This Number is assigned by using MAX(seq_number)+1 from the table where the…
pOrinG
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In Trimmomatic is there any default values for sliding window?

If I give a command for AVGQUAL:20 without sliding window will it set any default values for the slidingwindow?
Vaisakh Viswanath
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Algorithm for piecing together a sequence from multiple fragments

I am working on a real-time embedded system. I am trying to create a detailed timing analysis. I have collected runtime data, recording the start and stop time of each interrupt. Each burst of data looks something like this ISR# time ----- …
AShelly
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Analysis of DEXSeq count table

I am using a platform "Bcbio" for processing RNASeq fastqs. At the end of the process, it generates a number of files like counttables, sailfish raw data and so on. There is also a file called "combined.dexseq" which looks like; id Control_rep1_1 …
Fırat Uyulur
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Sequentially reduce values in a column in R

I am currently trying to reduce the values in a column by a certain total amount, until that amount reaches zero. For example, in the data frame created by this code: df = data.frame(matrix(0,nrow=10,ncol=2)) colnames(df) <- c("AccountNumber",…
Nick
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Forcing google map api 3 calls to occur in sequence

I'd like to load an overlay and then zoom to a predefined view. This works, but sometimes when the overlay is large, the zoom happens first. Even with the listener waiting for "idle" before zooming, sometimes it happens out of sequence. Any way to…
user3078869
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Grep outputting strange characters using -A and -B flags for fastq analysis

I have a file that looks like this: @HISEQ:331:C85AMANXX:8:1101:16636:1980…
The Nightman
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How to create Kubernetes cluster serving its own container with SSL and NGINX

I'm trying to build a Kubernetes cluster with following services inside: Docker-registry (which will contain my django Docker image) Nginx listenning both on port 80 and 443 PostgreSQL Several django applications served with gunicorn letsencrypt…
thibserot
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python to change '|' into tab delimenated

I need to replace '|' into tab so that I can analyze my human annotation genomic data (200+mb). I'm a research assistant learning how to analyze/manipulate sequencing data in the easiest/simplest way so that I can replicate this on more data. Here…
Jan Shamsani
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shorten numbering e.g., 1,2,5,6,7 becomes 1,2,5-7

I have been tasked with shortening a sequence of numbers by replacing internal sequences of 3 or more with a dash for the internal numbers (as in, 3,5,6,7,8,10 would be 3,5-8,10)
gordon
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Create output file names based on input file name in OSX

I have this script annotatepeaks.pl file mm9 -annStats filename > output I use this script to run one job: annotatepeaks.pl file.xls mm9 -annStats file_stat.xls > file_ann.xls Since I have multiple files and want to run in batch (add…
Duy Pham
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Processing FASTQ files based on mate pair length

The following files are two mates of a paired-end fastq file, I want to separate each fastq based on their…
Tahmtan Ebrahimi
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ValueError: need more than 0 values to unpack(python lists)

I'm getting an error while I'm writing my code tmp = c.pop(0) # taking out the first element from the list as the starting point complete = tmp[0][-1] print(complete) while c != []: complete += tmp[1][-1] [index] = [] for i, pair in…
Jessi
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SQL to generate next sequence in an alphanumeric id

I gained some help from this question, but still need some further assistance. I need to be able to generate the next available 2-digit alphanumeric code. I cannot change the table definition, before you ask. I am working in T-SQL. So, for example,…
rlphilli
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Sequencing 2 lines of jQuery

I have the following lines of jQuery: // When dragging ends stop: function(event, ui) { // Replace the placeholder with the original $placeholder.after( $this.show() ).remove(); // Run a custom stop function specitifed in the settings …
AnApprentice
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