Hi SRA team, I have a question of how to check the integrity of the BAM or FASTQ files. The .sra.vdbcache files were downloaded using prefetch and validated using vdb-validate. But how can I check whether the extraction of BAM or FASTQ files from .vdbcache was complete and did not ...
10x BAM to FASTQ converter Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. The FASTQ files emitted by the tool should contain the same set of seque...
The FASTQ files output bybamtofastqcontain the same set of sequences that were input to the original pipeline run, although the original order will not be preserved. 10x Genomics pipelines are generally insensitive to the order of the input data, so you can expect nearly identical results when...
Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. Forensic Sci. Intl. Genet. 21 (2016):68-75.S.L. Friis, A. Buchard, E. Rockenbauer, C. Borsting, N. Morling, Introduction of...
it had to work on a broadly used data format. Given that querying MCS in fastq files is time-consuming (> 1 min / MCS), we designed BamQuery to work on bam files in five steps (Fig.1a, and “Methods”): (1) reverse translation of each MAP into all possible MCS; (2) mapping...
December 2015Available online 12 December 2015Keywords:Next generation sequencingMassive parallel sequencingSNP–STR sequence analysisForensic geneticsSTRinNGS Python applicationThis work introduces the in-house developed Python application STRinNGS for analysis of STR sequenceelements in BAM or FASTQ f i les...
Learn about SAM & BAM files and how to read your raw alignment format in this blog, perfect for bioinformatics beginners.
PetaGene’s genomic data compression software will cut your storage costs and transfer times for BAM or FASTQ files stored on-premise or in the cloud.
Fast and easy, obtain significant insights starting from FASTQ files with OmicsBox. End-to-End Genetic Variation studies all in the same platform. Versatile Data Handling and Integration Gain a unified and complete dataset by integrating multiple VCF files, and ensure data integrity with efficient ...
Fastq FormatAPOBEC3MappingApolipoprotein B mRNA editing enzyme, catalytic polypeptide-like3 (APOBEC3), is a well characterized enzyme that attacks virus genome replication cycle such as HIV, SIV, HBV, leading context dependent G-to-A changes, referred to as "hypermutation." Several methods have ...