PASA Activity
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Activity for PASA
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Amol Ghodke posted a comment on discussion Help
I ran PASA pipeline on my data. but in log file i am getting following type of messeges...
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Hi, I am new for genome annotation. and recently started using PASA. I was running...
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Pengcheng Yang posted a comment on discussion Help
I have resolved this problem. The gmap and blat should be in the PATH variable.
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I have encountered the same problem. In the sample_data directory: ../scripts/Launch_PASA_pipeline.pl...
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PASA released /OLD_VERSIONS/PASA2-r20130425beta.tgz
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Brian Haas committed [r908]
bypassing rare error in merge step
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update
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add
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update
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update, non-fatal error if not finding annot up...
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ignoring lines that lack transcript_id value
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update, ignore # header/comments in gff3 parsing
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updated
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add
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add
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update
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update
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add
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recursively traverse alt isoforms to BED format
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add
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use cursor instead of putting all results in ram
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further fine-tuning for multithreading
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added multithreading to annotation comparison step
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update
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add
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turning off transactions, since they deadlock b...
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improved gtf-to-gff3 conversion and pasa gff3 v...
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ensure unique model IDs for alt isoforms
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ensure novel gene identifiers are unique each r...
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added SAM output flag
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option to turn off chimeric alignments
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no space before prime partial in gff3 output
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reset connection on Lost connection to server t...
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notes from Mike
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update
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add
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cut release
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prep for release
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update
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dbi to cgi
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dbi to cgi
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rename to cgi file
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updated to leverage the new Trinity assembly ac...
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update from Alexie, force phase val as int
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adding symlink to PerlLib
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no ouputting of stderr to stdout
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update
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no stderr to stdout
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Jane posted a comment on discussion Help
Hi， I am a senior student in Shenzhen University,China.My major is Biology Science...
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make compatible with new Trinity accession form...
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Rashmi posted a comment on discussion Help
Hi When i try to run run_sample_pipeline.pl I get following error: Processing CMD:...
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bugfix - allow for just using the imported gff3...
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bugfix to update query
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added --IMPORT_CUSTOM_GFF3 to sample run for te...
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password requires -p , bugfix
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need 0 for color in bed output for compatibilit...
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bugfix for bed generator
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update
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add
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Alexie committed [r856]
make: create bin if it doesn't exist (git issue...
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set max intron length to 500k
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remove assembly directory
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reduced some more user interface print outs
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or debug...
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update to FL print out to screen only if $SEE
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replaced that nada with dev/null
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just some more user-firendly printing of counter
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loading counter printed less frequently (my hom...
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template is more easily understood by average user
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create_mysql now works without a password too
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fix lib path
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update
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turned off extended AT-donor site check by default
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add
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added signal catcher for multithreading, accord...
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