Wiki » History » Version 3
Katie Lennard, 03/25/2022 09:03 PM
| 1 | 1 | Katie Lennard | # Wiki |
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| 3 | # Data location |
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| 5 | The data was transferred using Globus connect and Ilifu's Globus endpoint from a PC setup in cbio to Ilifu: |
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| 7 | `/cbio/users/katie/Nono/metagenomics |
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| 8 | ` |
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| 10 | The data has already been cleaned and decontaminated (human) by BGI, who have also performed a full analysis on the data (see files section) |
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| 12 | The full BGI results can be found together with the cleaned reads on Ilifu. |
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| 13 | 2 | Katie Lennard | |
| 14 | # YAMP pipeline update |
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| 15 | 3 | Katie Lennard | The YAMP pipeline was updated with: |
| 16 | 1. the latest metaphlan DB, downloaded from https://zenodo.org/record/4629921#.Yji3YxNBzOR |
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| 17 | 2. the latest humann DBs (chocophlan and uniref), as described here https://github.com/alesssia/YAMP/wiki/Getting-started#notes-on-the-metaphlan-databases and first downloading the relevant singularity container with `singularity pull docker://biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7` |
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| 18 | The command executed, from within the github directory of the latest YAMP repo was: |
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| 19 | `singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download chocophlan full |
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| 20 | ./assets/data/chocophlan ` |
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| 21 | AND |
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| 22 | `singularity run biobakery/workflows:3.0.0.a.6.metaphlanv3.0.7 humann_databases --download uniref uniref90_diamond |
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| 23 | ./assets/data/uniref` |