Unrecognized format: Requires named integer vector, fastq filename, dada-class, derep-class, sequence matrix, or a data.frame with $sequence and $abundance columns. I hope you can help me, Thank you, Cheers, Maria// ArmOli Oct 21, 2021 ...
The sequence file obtained in FASTQ format was imported into the CLC Genomics Workbench (Version 20.0.4). The read counts of each sample were processed using the RNA-seq analysis tool and mapped to the reference human genome hg19 using default parameter settings. Differential expression was analyze...
Genome or transcriptome sequence reference (FASTA or minimap2 index) Variants File Megalodon requires a set of candidate variants for--outputs variants(provide via--variant-filenameargument; VCF or BCF). Outputs All Megalodon outputs are written into the directory specified with the--output-directory...
the percentage of apoptotic cells were assessed with Annexin V-Phycoerythrin (Annexin V-PE) and 7-Amino-Actinomycin (7-AAD) double staining (Fig.1; Additional file2: Fig. S1; Additional file1: Table S3) and subsequently coupled to flow...
The messenger RNAs (mRNAs) of articular cartilage from rats with or without the treatment of DAE were sequenced using Illumina paired-end sequencing technology. The raw reads were uploaded in the NCBI Sequence Read Archive (SRA) database under BioProject accession number PRJNA642711. As shown in...
Note, that database should be formatted as described in 4 step of Installation of CD-HIT-OTU-Miseq (this reformatting places sequences with more specific annotations are at the beginning of the file). You can download reformatted versions of Greengenes and Silva databases here. Specify a ...
The contact map is the primary data object on which the genome binning is performed. The map is derived from the assembly sequences chosen (scaffolds or contigs) and the corresponding Hi-C alignments BAM file. Assuming Pip-style invocation, a map for a library constructed using the MluCI res...
exportFasta (FALSE): Set exportFasta=TRUE if users want to export sequences of fusion reads 7. Create a supporting annotation RData file In this section, we describe details how to create a annotation RData for your own annotation. We use the annotations from Ensembl (ensembl.org) as examp...
The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, ...
In order forsamblasterto output the entire sequence for clipped reads, the input SAM file must have soft clipped primary alignments. samblasterwill output unmapped/clipped reads into a FASTQ file if QUAL information is available in the input file, and a FASTA file if not. ...