harish0201/ngs_analysis

My python scripts for Peanut sequencing project

Scripts for NGS analysis

For Transcriptome sequencing and Whole Genome Bisulfite Sequencing analysis

• This is the list of all the scripts used for sequencing projects.

script	function*
DNAprocess.py	a module used for DNA sequence processing.functions include: get reverse complementary sequence translate DNA sequence to Amio Acid
get_fastqc.py	used for get the fastqc report summary of all files (FAIL, WARN and PASS for each module). figures are excluded
fastq_length_filter.py	from trimmomatic result fastq files. classify reads with different length range based on the cutoff. output 2 types (long and short) fastq files
mstrg_prep.py	For merged transcript GFF file by stringtie, appending refgene ID to stringtie assigned gene ID (MSTRG.*) if the gene region includes a ref gene
get_trim_report.py	extract the trimming statistics from Trimmomatic log file
get_align_stat.py	extract alignment statistics from Hisat2
extract_assembled_id_from_stringtie.py	extract ref gene ID, transcript ID and assembled stringtie gene ID. (recommend to use mstrg_prep.py to avoid this step)
class_transform.py	transform result from OrthoMCL, classify by species within a category
reciprocol_blast_selection.py	Get the top hit pairs for reciprocal blast
get_MATS_result.py	handling rMATS result. Summarizing all the significant alternative splicing even from different output files from rMATS
counting_transcripts.py	counting the number of transcripts in GFF/GTF file.
extractGOfromGFF.py	extract GO ids from gff3 file
mirdeep_res_handle.py	read report.log files from mirdeep2.pl result
Pynut	My package for biological analysis.
---	---

* for specific requirement or usage, please look into the script file.