This repository contains the codes, summary notes and principal results generated for the understanding of the single-cell analysis pipeline of Nematostella vectensis.
It is used to generate an index that optimizes the search of sequences. It is necessary to be executed before the mapping.
This parameter was used to map the short reads from RNA-seq to the reference genome.
The program was used to generate a gene transfer file (.gtf) that could be used by Cellranger. This file indicates the location of the genes and could contain also information abut codin sequence regions.
This program was used to give annotation to the proteins obtained from Transdecoder using the interpro database.
In summary, this command line instruction loads samtools and then uses it to filter a BAM file, keeping only properly paired reads (those that align correctly with their mate in the expected orientation and distance), excluding unmapped reads, and only including reads with a mapping quality score of 20 or higher.
This annotation tool is also used to get information about the sequences obtained from Transdecoder, it maps them to orthologous groups and functional terms from the eggNOG database
This program is used to filter out sequences that do not meet certain quality parrameters. Those sequences are discarded in order to avoid alterations in the downstream analysis.
Uses star to generate an index for the later mapping.
Maps the RNA reads to the built reference. It will generate at the end a count matrix that contains the RNA-counts (genes) associated with individual cells.