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Launched: Genozip 15 with co-compression of BAM and FASTQ
I am excited to announce the launch of our new version of Genozip - Genozip 15 - a genomic compressor for FASTQ, BAM, VCF and many other genomic formats....
Last edited by divon; 06-29-2023, 12:16 AM. -
FASTA and FASTQ: A Guide to Key File Formats for Sequencing Data
Performing successful sequencing analysis requires an understanding of different file formats and how they are used for various applications. Scientists interested in completing their own sequencing analysis should learn the purpose and contents of each format. In the next two articles, we will explore some of the essential file formats used in sequencing data analysis and their significance in the field.
FASTA
The FASTA file format is one of the most... -
Introducing Genozip - genomic file compressor
I would like to introduce a compression software package I developed: Genozip (www.genozip.com).
It is a tool with the primary objective... -
Can all R1 and R2 files be combined prior to interleaving?
My questions is whether it's okay to to combine multiple R1 and R2 fastq files (i.e. resulting in two files: R1.fastq and R2.fastq), and then use those... -
Combining fastq files from paired-end WES prior to trimming and alignment
Hi there!
I've tried to find answers to questions that apply to my scenario, but I'm still unsure about the kosher way to approach this....Last edited by reliscu; 05-08-2021, 12:34 PM. -
Lose of paired-end info after samtools markdup
Hi all,
I just did some paired end ATAC-seq and I have been trying to analyse the data. I align with Bowtie, remove mitochondrial reads,...Last edited by ishtiaqueh; 04-20-2021, 04:19 PM. -
Splitting a FastQ file into two
Hello folks,
I happen to have a small problem which seemed to be trivial at first, but keeps me busy for a while now already. Maybe you... -
bbduk and removing adapters of varying length
I am analyzing some published Tn-seq data. There appears to be residual transposon sequence in the reads, preventing alignment. Unfortunately, this sequence... -
FASTq from Torrent Server
Do Fastq files exported from IonTorrent Server have adapters and barcodes already removed? Should I use cudapt or trimmomatic to get rid of them? -
Re-mapping contigs or predicted genes?
Hi!
I'm quite new to bioinformatics and am currently running into a dilemma on how to approach my re-mapping.
I have successfully assembled... -
Need Help! Vsearch fastq_filter quality value above qmax
Hello all!
I'm new to the community and just started my first bioinformatics project. I'm filtering out merged reads with the expected... -
Exact duplicate reads/readnames/quality/tiles in Novaseq FASTQs
Anyone seen this? Some (not correlated with software versions AFAICT) of our MarkDuplicates jobs are failing because there are exact copies of the same... -
Split paired end multi-sample fastq to single-sample fastq
Hi,
I have a single, multi-sample FASTQ file containing paired end reads from dozens of samples. I would like to split this file into... -
add UMI sequences to fastq read name
Dear all,
I have paired-end fastq data generated with Illumina bcl2fastqv2.19 & sequenced on a Novaseq.The i5index is 7bp long, the... -
Determine mapping percentage from .fastq file
Is it possible to obtain the mapping percent from .fastq file?
If I do the following:
grep "@HISEQ" -c file.fastq...
