Question: What's reasonable to delete following a successful PASA run?

[Kris Alavattam]

Hi Brian,

Do you have any thoughts on what files and/or directories could be OK to delete following a successful run of PASA Launch_PASA_pipeline.pl and scripts/build_comprehensive_transcriptome.dbi? (And not wanting to rerun those script from any intermediate steps.) Apart from the contents of the *.compreh_init_build directory, is there anything else I'd want to potentially hang onto?

Thanks,

Kris

Current files and directories in an experiment directory (alignment with gmap, blat, and minimap2):

```txt

__pasa_trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite_SQLite_chkpts
__pasa_trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite_SQLite_chkpts.cmds_log
11.ooc
alignment.validations.output
blat.spliced_alignments.gff3
cleaning_1
err_seqcl_trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.log
gmap.spliced_alignments.gff3
gmap.spliced_alignments.gff3.completed
minimap2.splice_alignments.gff3.ok
minimap2.spliced_alignments.gff3
outparts_cln.sort
pasa_run.log.dir
pblat_outdir
Saccharomyces_cerevisiae.R64-1-1.108.gff3
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.chr-rename.fasta
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.chr-rename.fasta.cidx
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.chr-rename.fasta.fai
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.chr-rename.fasta.gmap
Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.chr-rename.fasta.mm2
seqcl_trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.log
tmp-14477-99653-out
tmp-14477-99653-out.tmp.1
tmp-14477-99653-out.tmp.2
tmp-14477-99653-out.tmp.3
tmp-14477-99653-out.tmp.4
tmp-14477-99653-out.tmp.5
tmp-14477-99653-out.tmp.6
tmp-14477-99653-out.tmp.7
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_1_EndToEnd.Trinity.accessions
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.align_assembly.config
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.build_comprehensive_transcriptome.stderr.log
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.build_comprehensive_transcriptome.stdout.log
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.compreh_init_build
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.Launch_PASA_pipeline.stderr.log
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.Launch_PASA_pipeline.stdout.log
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.assemblies.fasta
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_blat_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_blat_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_gmap_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_gmap_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_minimap2_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.failed_minimap2_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.pasa_alignment_assembly_building.ascii_illustrations.out
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.pasa_assemblies_described.txt
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.pasa_assemblies.bed
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.pasa_assemblies.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.pasa_assemblies.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.polyAsites.fasta
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_blat_alignments.bed
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_blat_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_blat_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_gmap_alignments.bed
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_gmap_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_gmap_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_minimap2_alignments.bed
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_minimap2_alignments.gff3
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.pasa.sqlite.valid_minimap2_alignments.gtf
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.cidx
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean.cidx
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean.fai
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean.mm2.bam
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean.mm2.bam.bai
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.clean.mm2.bam.ok
trinity_5781-5782_Q_IP_merged.trim-rcor.multi-hit-mode_100_EndToEnd.transcripts.fasta.cln

```

[Brian Haas]

Hi Kris,

You might want to hold onto the pasa.sqlite.pasa_assemblies.*, pasa.sqlite.assemblies.fasta, and sqlite database (*.sqlite).  If you don't plan on using pasaweb, then you could exclude the sqlite database.

If you're curious about what alignments made it or didn't make it into the pasa assemblies, you might hold on to 'alignment.validations.output' too.

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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas