cellranger mkfastqdemultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. It is a wrapper around Illumina's bcl2fastq, with additional useful features that are specific to 10x libraries and a simplified sample sheet format. cellranger counttakes FASTQ files fro...
It is a wrapper around Illumina's bcl2fastq with additional features that are specific to 10x Genomics libraries and a simplified sample sheet format. spaceranger count takes a microscope slide image and FASTQ files and performs alignment, tissue detection, fiducial detection, and barcode/UMI ...
faa, gz, fasta, zip, tar, jsonl, fa, fastq, gbff, tsv, txt, gff, fq, dll, fsa, pdb, json, gff3, ffn, rar, mpfa Related links: Wikipedia FASTA Page, Wikipedia FASTA Format Page an fna DNA and Protein Sequence Alignment is a special file format and should only be edited and sa...
Sequence or SEQ is the actual read sequence. Should generally follow the sequence line from the source FASTQ Quality String or Qual should generally follow the quality string from the source FASTQ file and be Phred-scaled. Predefined Tags these will be encoded tags that are predefined in the SA...
(GNU zip) is only capable of compressing a single file. If you open these files in a text editor, you will see only illegible characters. A typical file size is 1 MB. The file type was developed 10 years ago and is still in use today. Such GZ files store data aboutfastq,genomic,...
Read set –A read set is an abstraction of genomics reads, which are stored in FASTQ, BAM, or CRAM formats. Read sets can be imported into sequence stores and annotated with metadata. You can apply permissions to read sets using attribute based access control (ABAC). Reference –A genome...
The process of basecalling involves reading the signal data and converting this into fastq files containing the nucleotide sequences and associated quality scores from the sequenced molecule. It is also possible to store basecalled reads in BAM format directly from MinKNOW. You can find out more ...
(For more, see the full post on the blog: http://mozillascience.org/what-else-is-needed-for-code-reuse/) When we first started discussions around our latest "Code as a research object" project, one of the main topics that arose was reuse...
Read set –A read set is an abstraction of genomics reads, which are stored in FASTQ, BAM, or CRAM formats. Read sets can be imported into sequence stores and annotated with metadata. You can apply permissions to read sets using attribute based access control (ABAC). Reference –A genome...
cellranger mkfastqdemultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. It is a wrapper around Illumina's bcl2fastq, with additional features that are specific to 10x Genomics libraries and a simplified sample sheet format. ...