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Questions tagged [sequencing]

137 questions
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Is sorting necessary for merging BAM files using BamTools?

I have a pair of Illumina paired-end read files (say, A_1.fastq.gz and A_2.fastq.gz) produced from a single bacterial isolate for variant calling. First of all, I used FLASH to merge overlapping reads because of the read length (100 bp), insertion…
Wan
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parsing information out of sequencing data

I have a txt file that is a converted fasta file that just has a particular region that I'm interested in analyzing. It looks like…
James Weger
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looking for specific patterns between two strings in python - fastq file - sequencing reads

I’m trying to write a code in python that will help me look for a string between two specific strings. When I implement the code with a single string, I get the desired output. However, I need to match the pattern in an array of sequences. It keeps…
user8033590
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eliminate empty files in a subroutine in perl

I want to a add a code in the next script to eliminate those empty output files. The script convert a single fastq file or all the fastq files in a folder to fasta format, all the output fasta files keep the same name of the fastq file; the script…
abraham
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How to get RPKM value from bed file or wig files? And what's the difference between these two type of files?

I want to download fastq raw file from RNAseq to get gene expression values. But GEO only provides .bed.gz and .wig.gz formats. What can I do to get the RPKM values? Thank you very much!
Zhili
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Package version GUID in App-V 5.1

I'm working with App-V 5.1. I'm interesting in what does "Package Version GUID" in the [Change History] tab mean? This value is different from "Package version GUID" in [Properties] tab. Also, I cannot find this value after adding package;…
Yuriy Rozhkov
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Improve performance of python script to filter unpaired reads in a pair of FASTQ files

I have some paired end sequencing data. However, the files are not properly paired. There are unpaired reads which need to be removed to make the read pair files consistent. Though there are solutions like using Trimmomatic. I want suggestions as to…
Parashar
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Visualizing data using CoMut

My question is about visualizing mutations of cohort of samples, something exactly like coMut map (https://www.broadinstitute.org/blog/visualizing-cancer-genome). Does someone know if there is a specific website for making these type of plots?…
Armo
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Best way to get precise timing on iOS for sequencing musical notes

So I'm trying to write a basic music sequencer sort of thing. Something that needs very precise timing. This is for iOS 9. I'm using libpd (Pure Data) right now, just sending in events with various delays to achieve the effect I'm after. And it…
Josh Knowles
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how do i sequence methods in libgdx

I am using libgdx and i have several game objects with different methods i want the methods in my timer to happen one after another but in libgdx they happen all at once i dont know how to fix it timer.scheduleTask( task = new Task(){ public…
ChukaApps
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What do Illumina HiSeq/MiSeq paired end reads look like?

My understanding is that paired end reads from the Illumina HiSeq/MiSeq platforms looks something like this: R1: AAAAAACCCCCC R2: GGGGGGTTTTTT Where the reads found in R2 are the reverse compliment of those found in R1. This does not appear…
The Nightman
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Using python to compare differences in strings from an input fastq file

I would like to edit a sequencing Fastq file, and delete lines that are repetitive only at certain character positions. Ideally I would iterate over every line in the input file and output a file that has only a single instance of any unique set of…
The Nightman
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Scorm 2004 3rd Ed - Limit Attempts

I am trying to limit the number of attempts that a user can take to pass a quiz, regardless of content launch number. I found a precondition rule, but i think that is only for the current launch attempt. Has anyone successfully done this? The sco…
Duncan
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Binning Together Allele Frequencies From VCF Sequencing Data

I have a sequencing datafile containing base pair locations from the genome, that looks like the following example: chr1 814 G A 0.5 chr1 815 T A 0.3 chr1 816 C G 0.2 chr2 315 A T 0.3 chr2 319 T C 0.8 chr2 340 G C 0.3 chr4 514 A G 0.5 I would like…
The Nightman
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Extracting specific information from a Fastq file for Sequencing Analysis

My goal is to extract pieces of data from genome sequencing Fastq files and plot them. I would like to get the identifying information for each sequencing read and then two pieces of information about the read. Below I have pasted two reads from a…
The Nightman
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