Andromeda Clean Up Fall 2022

16S_E5

I deleted the raw files becasue these also exist in my github lab notebook. These are trial 16S files from the E5 team and I believe also exist at Shedd with Ross. The lab work was not done or sequenced at URI.

Acc_dy

This appears to be some fasta file.. with protein codes? Where did this come from? Deleted it. Possibly from protein expression from Erin M?

BleachingPairs_16S

Raw data files are on NCBI for this project.

BleachingPairs_ITS2

Raw data was deleted b/c this exists on NCBI and data analysis is complete.

BleachingPairs_RNASeq

Data analysis is still in progress so I did not change anything here. There is no raw data here.

BleachingPairs_WGBS

cd BleachingPairs_methylseq/. this is the old genome v2 version so I can delete the biggest folders:

• bismark_deduplicated
• reference_genome

I ended up deleting the whole folder to just leave the v3 version.

raw_data is all sym links.

The rest I will leave until all analysis is done.

HoloInt_16s

I went to delete the HoloInt_16s/raw-data folder because there are on NCBI but I got this question: rm: remove write-protected regular file ‘raw-data/HPW061_S56_L001_R1_001.fastq.gz’? so I exited out of this for now…

HoloInt_ITS2

No raw data here. This is all on NCBI

HoloInt_WGBS

I am out of the testing trial phase and using genome v2 version so I can delete the biggest files and whole folders.

cd HoloInt_methylseq, HoloInt_methylseq2, HoloInt_methylseq3, and HoloInt_methylseq_final, . this is the old genome v2 version so I can delete the biggest folders:

• bismark_deduplicated
• reference_genome

Old Genome files

I removed:

• Montipora_capitata_HIv2.assembly.fasta
• Montipora_capitata_HIv2.genes.gff3
• Pocillopora_acuta_HIv1.assembly.fasta

Where does this live outside of my folders? /data/putnamlab/estrand/PointJudithData_16S/QIIME2_v4v5/gut_v4v5/00_RAW_gz

PointJudithData_16S

We are only using V6 region so I am deleting the analysis I did for V3V4.

rm -r QIIME2_v4v5

PointJudithData_MBDBS

This is still in progress so nothing to delete here.

SymPortal

I deleted this folder b/c I can redownload this for a future analysis using script I already have.

Test_V3V4_16S

This is the only spot for this raw data so I didn’t delete any of it.

work

This didn’t have anything important in it.. I think this was a product of a methylseq run in the wrong directory? Deleted.