Questions tagged [fastq]

FASTQ is a file format use to store short reads and their quality values

Filter by
Sorted by
Tagged with
9 votes
1 answer

How to get the count of each kmer past 255 using khmer

I have a Fastq file and I want to get the exact count of each possible kmer from this file. On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
hilta007's user avatar
  • 173
2 votes
1 answer

efficient counting of dinucleotides/trinucleotides on fastq reads?

What's an efficient way of counting of dinucleotides/trinucleotide pattern on fastq.gz file reads? I know there are tools like seqtk that will be very efficient at reading through the .fastq.gz files,...
719016's user avatar
  • 2,324
6 votes
2 answers

5' and 3' bias in Rna-seq data

I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
stack_learner's user avatar
3 votes
3 answers

How to demultiplex pair-end fastq reads with barcode 2 in the identifier line?

I have multiplexed pair-end fastq reads with dual barcodes. The issue is that one barcode is present in the header and one is present at the beginning of the read. I need a method to demultiplex this ...
Caleb Benson's user avatar
3 votes
1 answer

Can the canu assembler output a fastq file of the final assembly just like HGAP4?

I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
Biomagician's user avatar
  • 2,459
7 votes
2 answers

Canu assembly not making a single consensus?

I've downloaded reads from this BioProject. Using canu with default parameters (no correction), I've got 4 contigs, none of which really look like the reference plasmid here. The command I used was: ...
thestatnoob's user avatar
5 votes
1 answer

Estimating BAM file from compressed fastq file size

Is there a way to estimate the size of a BAM file will have after mapping with BWA? The input file are two mates fastq files, compressed with gzip, each one about 70G.
gc5's user avatar
  • 1,783
4 votes
2 answers

Is there a way to quickly verify the presence of some SNPs in Fastq files?

Is there a tool that can scan fastq files without assembling them for a custom list of user defined snps?
Dan K's user avatar
  • 89
7 votes
1 answer

Split FASTQ and matching BAM into matching chunks

I am running a slow downstream analysis on a large set of nanopore reads (approx 3 million), and would like to split them into smaller chunks, run the analysis in massively parallel, and then ...
Scott Gigante's user avatar
13 votes
2 answers

How to convert fastq to fast5

fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract ...
aechchiki's user avatar
  • 2,676
6 votes
2 answers

How can I edit a specific FASTQ read in place, given the read ID?

I am introducing SNVs into specific samples in order to estimate false negative rates for a variant calling pipeline. I know reads can be simulated but I would actually prefer to use the real data so ...
dkainer's user avatar
  • 128
9 votes
1 answer

FASTQC overrepresented sequences after trimming

I have a set of RNA-seq samples from different experiments (Single and Paired End, depending on the experiment). I ran FASTQC in all the samples and found overrepresented adapter sequences: I removed ...
plat's user avatar
  • 1,022
7 votes
3 answers

Extract nanopore read ID & start times from fastq file

I have a fastq file from minION (albacore) that contains information on the read ID and the start time of the read. I want to extract these two bits of information into a single csv file. I've been ...
roblanf's user avatar
  • 952
6 votes
2 answers

How to safely and efficiently convert subset of bam to fastq?

Question How can I extract reads from a bam file (produced by bwa-mem) to fastq given a ...
Kamil S Jaron's user avatar
12 votes
8 answers

Fast way to count number of reads and number of bases in a fastq file?

I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
terdon's user avatar
  • 9,662
9 votes
2 answers

How do you generate read-length vs read-quality plot for long-read sequencing data (e.g., MinION)?

How do you generate read-length vs read-quality plot (heat map with histograms in the margin) for long-read sequencing data from the Oxford Nanopore Technologies (ONT) MinION? The MinKNOW software ...
Mark Ebbert's user avatar
  • 1,304
6 votes
1 answer

How to maximize fastq parsing with FastqGeneralIterator (Bio.SeqIO.QualityIO)

I'm contributing to a python-based project that uses Biopython to analyze fastq files. It currently uses SeqIO.parse, which ...
Mark Ebbert's user avatar
  • 1,304
20 votes
12 answers

Random access on a FASTQ file

I would like to select a random record from a large set of n unaligned sequencing reads in log(n) time complexity (big O ...
winni2k's user avatar
  • 2,236
21 votes
10 answers

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

I used to work with publicly available genomic references, where basic statistics are usually available and if they are not, you have to compute them only once so there is no reason to worry about ...
Kamil S Jaron's user avatar
14 votes
3 answers

How can I improve the yield of MinION sequencing runs?

This is a frequently-asked question within the nanopore community. Oxford Nanopore currently claims that they are able to generate run yields of 10-15 gigabases (e.g. see here and here), and yet it's ...
gringer's user avatar
  • 13.8k
7 votes
1 answer

The effects of incomplete bisulfite conversion upon mapping efficiency

This question has also been posted on Biostars I have sequenced numerous multiplexed pools of BS amplicon-seq libraries derived from human samples on a MiSeq over the past few weeks. I have been ...
David Ross's user avatar
42 votes
4 answers

What is the difference between FASTA, FASTQ, and SAM file formats?

I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another? Based on Wikipedia pages, I can't ...
kenorb's user avatar
  • 1,313

1 2