Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
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Convert 10X VDJ .bam file to .fastq
I asked a similar question in the past regarding the conversion of scRNASeq .bam files to .fastq's, please refer to this link here: BAM to gene expression matrix (UMI counts per gene per cell),10X
I ...
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How can I convert all the bam files in a directory into fastq files using samtools bam2fq?
This question was also asked on Biostars
I want to find variants in the exome data. How can I convert all the bam files in a directory into fastq files using samtools bam2fq?
I couldn't find simple ...
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Is there some tool so find run accessions metadata?
I have a project in which I'll use some FASTQs to feed a neural network and, as label, I'll use the estimated age range. I've got the data from AMTDB, and there they have the metadata.txt, in which we ...
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Aligning FASTQs to FASTA reference
I'd like to align some FASTQs to an average mtDNA FASTA file that I have downloaded so I can have the human mtDNA isolated from those FASTQs. For that, I used bowtie2. Can I expect that after running ...
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How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?
I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some ...
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Downloading multiple SRA files as FASTQ files using SRA Toolkit
I was able to download all of the SRA files for a specific bioproject using the command:
prefetch -O output_directory --option-file SRR_Acc_List.txt
I then tried ...
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Compare FASTQ reconstructions to mtDNA
I have some doubts in how to proceed to compare ancient mtDNA with modern mtDNA. A little more context:
The problem:
I have some FASTQs associated with a given FASTA. They contain mtDNA. My goal is to ...
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Aside from the header info, is there any way to distinguish between sequences generated by MiSeq and MiniSeq platforms?
I am comparing Illumina MiSeq (using MiSeq v3 kit) and MiniSeq (MiniSeq High Output kit) instruments for sequencing E.coli and Salmonella. I am curious if there is any way to bioinformatically ...
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How to know if FASTQ/BAM is from reference genome (FASTA)?
I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
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Fastq file with very high per base sequence quality and no box-whisker plot
I have my data from NCBI. I am having difficulty making sense of and correlating my fastq file read 1 and read 2 and the fastQC report. As shown below, I have two paired-end read results each ...
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Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline
In a FastQ to BAM pipeline where only adapter trimming is performed, I've noticed a potential discrepancy in read counts between the initial FastQ files and their resulting BAM file. Specifically, I'm ...
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Parameter optimisation of minimap2
I'm leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files.
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Shell script to validate fastq issue
I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one ...
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Multiple SRR ID downloaded for single GSM IDs input issue
So here I'm trying to donwload multiple fastq files based on the GSM ID input the script works fine when then input is only SRR id but it runs into error when it is given GSM ID
My small GSM ID input ...
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ncbi fastq dump error in loop
I have a very basic objective which I want to give list of id to a ncbi-srafastq tool kit which will prefetch the id which is in .sra file extension and then it will run fastq-dump on the file to ...
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