Open punching-samuel opened 1 month ago
And about the '/output/res/temps_files', I checked the try_1_rna_count.csv,
Peptide 2_STAR_sample-1 2_STAR_sample-2 2_STAR_sample-3 2_STAR_sample-4 2_STAR_sample-5 2_STAR_sample-6 1 ASLLDVFVLTR -2 -2 -2 -2 -2 -2 2 ATMELYQISQR -1 -1 -1 -1 -1 -1 3 AVALINAAIQK -1 -1 -1 -1 -1 -1 4 AVIQVSQIVAR -1 -1 -1 -1 -1 -1
All the values in the table are Negative numbers, could you assist me in understanding this situation? I'm looking for clarification and would greatly appreciate your guidance in explaining it further. Thank you in advance for your help.
Samuel.
I select only 50 peptides in peptides.tsv to run bamquery. The output seems correct.
The output directory already exists in this path.
BamQuery analysis will continue where it left.
Treatment File : Done!
Reverse Translation : Done!
Alignment : Done!
common_to_modes : Done!
Getting counts for 8 samples
***** WARNING: File xxx/Software/bamquery/lib/genome_versions/genome_v38_104/gencode.v38.primary_assembly.annotation.gtf has inconsistent naming convention for record:
GL000009.2 ENSEMBL gene 56140 58376 . - . gene_id "ENSG00000278704.1"; gene_type "protein_coding"; gene_name "ENSG00000278704"; level 3;
***** WARNING: File xxx/Software/bamquery/lib/genome_versions/genome_v38_104/gencode.v38.primary_assembly.annotation.gtf has inconsistent naming convention for record:
GL000009.2 ENSEMBL gene 56140 58376 . - . gene_id "ENSG00000278704.1"; gene_type "protein_coding"; gene_name "ENSG00000278704"; level 3;
========== Genomic and ERE annotation summary by position : Done! ============
========== Genomic and ERE annotation by peptide : Done! ============
========== Transcription based biotyping by sample: Done! ============
========== Transcription based biotyping by group sample: Done! ============
========== BamQuery : Done! ============
But I still want to ask that if there sets the limited maximun numbers for peptides in peptides.tsv? My total 3617 peptides have total 1107 alignments, which means nearly 2/3 peptides not aligned? How to optimize the situation? Thank you in advance for your help.
With regards. Samuel.
Hello, I run bamquery
And my output is as follows,
It looks that the process is still running and hasn't finished yet, but my log file hasn't updated at all. My log as follows,
I will appreciate it if you can upload or show some standard log or the information about the intermediate stages.