Bohoon Shim

Adapter Trimming on PE reads have different number of reads output

1

Hello, trim_galore -o output --fastqc --paired $R1_file $R2_file I have utilized trim-galore to trim illumina adapters on my PE sequencing reads. When I tried to process the output fq files...

Cellranger Data Loading

1

While loading the cellranger data (10X), this is the error I encounter. -- [4/14] Parsing "/jsimonlab/users/bshim/Shuntaro_scRNA_TCR/Pool142_Cellranger/Pool142_Pt1_R/outs/all_contig.bam.bai" -- Warning: line 1 appears to contain an embedded nulError in stri_trim_both(string) : invalid...

Prepare ORFs step

1

I had a question regarding preparation of all candidate ORFs from annotated transcript regions. I was wondering why only 3 frame translation is conducted to pull out candidate ORF. If...

Ribotricer Output

4

Hello, I am trying to merge two list of ORFs predicted by the RibORF algorithm and Ribotricer Algorithm. I am aware that RibORF predicts ORFs at the transcript level while...

ORF Annotations

1

Hello, I was wondering if there is a way to further break down ORF annotations presented by the ribotricer algorithm. I would like to get a sense for proportion of...

QTI-Seq vs TI-Seq

1

Hello, I would like to conduct a differential analysis at TI level but data that I have available is restricted to LTM treated TI Seq data (GTI-Seq). I am aware...

Unique Mapper

3

Hello, Does Ribotish also only consider uniquely mapped reads similar to lot of other ORF prediction algorithms based on RiboSeq data? Is there a way to incorporate multimappers? I am...

-a option

12

Hello, I have a custom stringtie derived GTFs that I am trying to predict ORFs from. I am also inputting the primary assembly gene annotations from gencode with option -a...

Predict Error

11

I inputted candidate ORF text file to narrow down the list of ORFs of interest with the TI Seq data. I am receiving this error after running predict. Candidate ORFs...