James Vire

Christian, I'll try out the BTLib indexer tool. If all else fails I still have the pre-generated Arabidopsis matrix provided. Thank you for this neat tool and all your generous help. Thank you, James

Thank you Christian, Perhaps I am confused about the purpose of the database files. If I understand correctly the refseq and embl sequences (in this case all of the asterid taxon) are for training the HMM: - database files are: /home/loki/Desktop/ESTscan/db/refseq/release/plant*.gbff /home/loki/Desktop/ESTscan/db/embl/*.dat Extracting asterid sequences from the refseq and embl databases yeilded ~1 GB of extracted sequences. Next, comes the UniGene clusters, which I'm not entirely sure what purpose...

Hi all, I am running into an issue I believe could be entirely due to misunderstanding what file to use for the $ugdata file. I wanted to download a .dat for all plants at the Unigene website: ftp://ftp.ncbi.nih.gov/repository/UniGene/ However, it looks like there only .dat files for specific species. I selected Helianthus (Asteraceae) and downloaded Han.data.gz (ftp://ftp.ncbi.nih.gov/repository/UniGene/Helianthus_annuus/Han.data.gz) and unziped it. When I ran: ./extract_UG_EST /home/loki/Desktop/ESTscan/Asteraceae.conf...

Thank you Christian! It looks like it ran without a hitch: loki@rnoyes-Precision-T3610:/usr/local/bin/estscan-3.0.3$ ./prepare_data -e /home/loki/Desktop/ESTscan/Asteraceae.conf Build ESTScan Tables for /home/loki/Desktop/ESTscan/Asteraceae.conf ------------------------------------------------------------------- Current parameters: - organism: Helianthus annuus - taxonomic level: asterids - database files are: /home/loki/Desktop/ESTscan/db/refseq/release/plant*.gbff /home/loki/Desktop/ESTscan/db/embl/*.dat...

Hi all, I am trying to generate matricies for the taxonmic level of Asterids. I successfully have extracted the mRNA. I am however running into an error during the masking of redundancy step. Below is the output: loki@rnoyes-Precision-T3610:/usr/local/bin/estscan-3.0.3$ ./prepare_data -e /home/loki/Desktop/ESTscan/Asteraceae.conf Build ESTScan Tables for /home/loki/Desktop/ESTscan/Asteraceae.conf ------------------------------------------------------------------- Current parameters: - organism: Erigeron...