You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hello,
I tried to find guidance on this online but was unsuccessful. I'm running an experiment using a custom oligo panel with my genes of interest, I've sequenced them using a MiSeq, and have already analyzed my data using salmon (mapping-based mode) using the following index:
This index is for the full transcriptome and I then used tximport with a t2gene file containing only my genes of interest. However, should I have created an index containing only transcriptome data for my genes of interest? Would this decrease the likelihood of spurious mappings?
reacted with thumbs up emoji reacted with thumbs down emoji reacted with laugh emoji reacted with hooray emoji reacted with confused emoji reacted with heart emoji reacted with rocket emoji reacted with eyes emoji
-
Hello,
I tried to find guidance on this online but was unsuccessful. I'm running an experiment using a custom oligo panel with my genes of interest, I've sequenced them using a MiSeq, and have already analyzed my data using salmon (mapping-based mode) using the following index:
grep "^>" <(gunzip -c GRCh38.primary_assembly.genome.fa.gz) | cut -d " " -f 1 > decoys.txt
sed -i -e 's/>//g' decoys.txt
cat gencode.v44.transcripts.fa.gz GRCh38.primary_assembly.genome.fa.gz > CRCH38_and_decoys.fa.gz
salmon index -t GRCH38_and_decoys.fa.gz -d decoys.txt -p 30 -i GRCh38_salmon_index --gencode
This index is for the full transcriptome and I then used tximport with a t2gene file containing only my genes of interest. However, should I have created an index containing only transcriptome data for my genes of interest? Would this decrease the likelihood of spurious mappings?
Thanks in advance for your response/help!
Beta Was this translation helpful? Give feedback.
All reactions