C elegans analysis for Victoria and Daniel

Splice Variant Analysis for LAT-1

Victoria

Exon quantification

• got exon positions from same genome annotation like mappings ../data/chromosom2_exons.bed
• count reads hitting exons with bathometer ../scripts/bathometer.sh
• output: FPKM values for each exon ../analysis/exon_quantification/exon_quantification.tsv
• File hochgeladen in webtool
• Exon-Name include Chromosom:Start-Stop , Strand, ParentTranscript
• "Parent-Transcipt" -> hierarchical because one CDS/transcript (parent) can have more exons (child)

Search specific sequences (found in RACE)

• count for each sequence and its reversed sequence ../data/sequence_and_reverse.txt
• normalise for read-coverage, proportion of these reads per sample:
  • ratio = count/allReads

Daniel

genes bathometer

• run bathometer for given bed file with genes ../analysis/20210816_genes_bathometer/run_bathometer.sh
• file hochgeladen in webtool

Figure LAT-1 splice variantes

• checked reproducability of Alex results:

worms

1.0 splice_variants_analysis.sh

• Step 1.1: StarIndex
• Step 1.2: Mapping with Star -> bam
• Step 1.2: Sort -> sorted.bam
• Step 2.0: Quantification with Stringtie -> gtf
• Step 3.0. Extract wanted gene (LAT-1) from results -> lat1.gtf

2.0 visualization_splice_variants.sh

• runs R script -> PFADE ÄNDERN

Fastqs per transcript result for cloning

• gtf2bed -> .bed -> sort for gene_id > getfasta from .fa > .fasta gtf2bed < lat1_d1_adult_gonad_wildtype_2.gtf > lat1_d1_adult_gonad_wildtype_2.bed cat lat1_d1_adult_whole_wildtype_4.bed | sort -k10 > lat1_d1_adult_whole_wildtype_4_sorted.bed bedtools getfasta -fi ../../../data/wbps14/caenorhabditis_elegans.PRJNA13758.WBPS14.genomic.fa -bed lat1_d1_adult_gonad_wildtype_5_sorted.bed -fo lat1_d1_adult_gonad_wildtype_5.fasta -name+