search

a2iEditing / RNAEditingIndexer

A tool for the calculation of RNA-editing index for RNA seq data
Other
36 stars 18 forks source link

high C2A and C2TEditingIndex #39

Open yulicarp opened 1 year ago

yulicarp commented 1 year ago

Why is there such a high C2A/C2TEiditingIndex value in my result? what went wrong?

my code

RNAEditingIndex -d /data/output/level_3_editing/bam/${sample} \
    -f hg38_2passMode_dedup.bam \
    -o /data/output/level_3_editing/level_3_AEI/${sample} \
    -l /data/output/level_3_editing/level_3_AEI/log \
    --genes_expression /bin/AEI/RNAEditingIndexer/Resources/GenesExpression/HomoSapiens/ucscHg38GTExGeneExpression.bed.gz \
    --refseq /bin/AEI/RNAEditingIndexer/Resources/RefSeqAnnotations/HomoSapiens/ucscHg38RefSeqCurated.bed.gz \
    --snps /bin/AEI/RNAEditingIndexer/Resources/SNPs/HomoSapiens/ucscHg38CommonGenomicSNPs150.bed.gz \
    -gf /bin/AEI/RNAEditingIndexer/Resources/Genomes/HomoSapiens/ucscHg38Genome.fa \
    -rb /bin/AEI/RNAEditingIndexer/Resources/Regions/HomoSapiens/ucscHg38Alu.bed.gz \
    --genome UserProvided \
    --paired_end \
    --stranded

result

StrandDecidingMethod,Group,Sample,SamplePath,A2CEditingIndex,A2GEditingIndex,A2TEditingIndex,C2AEditingIndex,C2GEditingIndex,C2TEditingIndex
StrandedData,Editing_Index_Unknown,,/data/output/../hg38_2passMode_dedup.bam,0.0113496080893,0.152915596519,0.00715928358272,0.34464189553,0.164001640016,0.318876176933
StrandedData,Editing_Index_Unknown,,/data/output/../hg38_2passMode_dedup.bam,0.0119108532335,0.190843078733,0.00662558030254,13.9161897653,0.723355412611,0.794523166623
SammiLyu commented 1 year ago

Hi @yulicarp

I am running into the same issue where my C2A and C2T editing indices are much higher than the A2G editing index. Just wondering, have you maybe found out what is the cause of the issue? Thank you so much in advance!

twinscorn commented 10 months ago

Hi, I think their Nature Methods paper mentioned that STAR two-pass alignment is not recommended because it will increase the noise level in this analysis