updated /home/data/metagenomics directory from /home/data/metagenomics-2310

for consistency, updated &USER text to <username>

Author: agomezncgr

03-FilteringRedAlder.Rmd

@@ -33,7 +33,7 @@ cd ~/microbe_fastq
 Link to the merged minion reads
 
 ```{bash,eval=FALSE}
-ln -s /home/data/metagenomics-2310/red-alder-reads/3469-3.all.fastq .
+ln -s /home/data/metagenomics/red-alder-reads/3469-3.all.fastq .
 ```
 
 ## Alignment
@@ -44,7 +44,7 @@ Run Minimap2 to align the MinION reads to the red alder genome
 
 ```{bash,eval=FALSE}
 minimap2 -x map-ont -L -t 8 -a \
-/home/data/metagenomics-2310/red-alder-reads/red-alder-genome.fasta \
+/home/data/metagenomics/red-alder-reads/red-alder-genome.fasta \
 3469-3.all.fastq > 3469-3-minionxredalder.mm2.sam
 ```
 
@@ -76,6 +76,6 @@ gzip 3469-3.microbe.fq
 Reads are here: 
 
 ```{bash,eval=FALSE}
-/home/data/metagenomics-2310/red-alder-reads/4956-3.all.fastq
+/home/data/metagenomics/red-alder-reads/4956-3.all.fastq
 ```
 

05-PycoQC.Rmd

@@ -19,7 +19,7 @@
 Where is it?
 
 ```{bash,eval=FALSE}
-/home/data/metagenomics-2310/red-alder-reads/sequencing_summary_FAS21661_9ac87089.txt
+/home/data/metagenomics/red-alder-reads/sequencing_summary_FAS21661_9ac87089.txt
 ```
 
 ## PycoQC package & code

07-KrakenUniq.Rmd

@@ -74,7 +74,7 @@ Take a look at the file using head.
 <details>
   <summary>Click for Answer</summary>
 ```{bash,eval=FALSE}
-head /home/data/metagenomics-2310/krakenuniq/library/bacteria/library_headers.orig
+head /home/data/metagenomics/krakenuniq/library/bacteria/library_headers.orig
 ```
 </details>\
 
@@ -84,23 +84,23 @@ How many sequences are there?
 <details>
   <summary>Click for Answer</summary>
 ```{bash,eval=FALSE}
-wc -l /home/data/metagenomics-2310/krakenuniq/library/bacteria/library_headers.orig
+wc -l /home/data/metagenomics/krakenuniq/library/bacteria/library_headers.orig
 ```
 </details>\
 
 How many sequences are Frankia?
 <details>
   <summary>Click for Answer</summary>
 ```{bash,eval=FALSE}
-grep -c Frankia /home/data/metagenomics-2310/krakenuniq/library/bacteria/library_headers.orig
+grep -c Frankia /home/data/metagenomics/krakenuniq/library/bacteria/library_headers.orig
 ```
 </details>\
 
 How many genera (field 2)?
 <details>
   <summary>Click for Answer</summary>
 ```{bash,eval=FALSE}
-awk '{print $2}' /home/data/metagenomics-2310/krakenuniq/library/bacteria/library_headers.orig | sort -u| wc -l
+awk '{print $2}' /home/data/metagenomics/krakenuniq/library/bacteria/library_headers.orig | sort -u| wc -l
 ```
 Note: this doesn't strictly give us the number of genera as some genera are written as Frankia_* and are counted independently even though they are all part of the Frankia genus.
 </details>\
@@ -109,14 +109,14 @@ And how many of each genera?
 <details>
   <summary>Click for Answer</summary>
 ```{bash,eval=FALSE}
-awk '{print $2}' /home/data/metagenomics-2310/krakenuniq/library/bacteria/library_headers.orig | sort | uniq -c | less
+awk '{print $2}' /home/data/metagenomics/krakenuniq/library/bacteria/library_headers.orig | sort | uniq -c | less
 ```
 </details>\
 
 ## Link to the krakenuniq database
 
 ```{bash,eval=FALSE}
-ln -s /home/data/metagenomics-2310/krakenuniq/ .
+ln -s /home/data/metagenomics/krakenuniq/ .
 ```
 
 ## Run KrakenUniq
@@ -135,7 +135,7 @@ conda activate krakenuniq
 Run Kraken on sample 3469-3.
 ```{bash,eval=FALSE}
 krakenuniq \
-	--db /home/data/metagenomics-2310/krakenuniq \
+	--db /home/data/metagenomics/krakenuniq \
 	--threads 32 \
 	--report-file 3469-3.report \
 	--unclassified-out 3469-3.unclassified.fq \

10-Centrifuge.Rmd

@@ -72,9 +72,9 @@ conda activate centrifuge
 
 ```{bash, eval=FALSE}
 centrifuge \
-  -x /home/data/metagenomics-2310/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
-  -1 /home/data/metagenomics-2310/centrifuge/ERR2271042_1.fastq \
-  -2 /home/data/metagenomics-2310/centrifuge/ERR2271042_2.fastq -t \
+  -x /home/data/metagenomics/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
+  -1 /home/data/metagenomics/centrifuge/ERR2271042_1.fastq \
+  -2 /home/data/metagenomics/centrifuge/ERR2271042_2.fastq -t \
   -p 4 \
   --met-file ~/centrifuge/centrifuge_results/ERR2271042_meta.txt \
   --met-stderr -S ~/centrifuge/centrifuge_results/ERR2271042_cent.out
@@ -84,12 +84,12 @@ centrifuge \
 You can also run all the samples together using a for loop (>1 hr).
 
 ```{bash, eval=FALSE}
-for i in /home/data/metagenomics-2310/centrifuge/*_1.fastq; do
+for i in /home/data/metagenomics/centrifuge/*_1.fastq; do
   bn=`basename $i _1.fastq`
   centrifuge \
-  -x /home/data/metagenomics-2310/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
-  -1 /home/data/metagenomics-2310/centrifuge/${bn}_1.fastq \
-  -2 /home/data/metagenomics-2310/centrifuge/${bn}_2.fastq -t \
+  -x /home/data/metagenomics/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
+  -1 /home/data/metagenomics/centrifuge/${bn}_1.fastq \
+  -2 /home/data/metagenomics/centrifuge/${bn}_2.fastq -t \
   -p 4 \
   --met-file ~/centrifuge/centrifuge_results/${bn}_meta.txt \
   --met-stderr -S ~/centrifuge/centrifuge_results/${bn}_cent.out
@@ -120,7 +120,7 @@ Create the report. We will use a for loop to generate the report for all the sam
 for i in ~/centrifuge/centrifuge_results/*_cent.out; do
   bn=`basename $i _cent.out`
   centrifuge-kreport \
-  -x /home/data/metagenomics-2310/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
+  -x /home/data/metagenomics/centrifuge/complete_genomes/Arc_Bac_Vir_Hum_Eupath_v2 \
   $i \
   > ~/centrifuge/centrifuge_krn_results/${bn}_cent.out.krn
 done
@@ -132,7 +132,7 @@ done
 Use awk to extract columns 2, 10, and 18 from the PRJEB23207 metadata file. Then, pipe the output to grep and exclude samples that were sequenced with the “Ion Torrent PGM” platform
 
 ```{bash, eval=FALSE}
-awk -F'\t' '{print $2,$10,$18}' /home/data/metagenomics-2310/centrifuge/PRJEB23207_metadata.txt | grep -i -v "ion"
+awk -F'\t' '{print $2,$10,$18}' /home/data/metagenomics/centrifuge/PRJEB23207_metadata.txt | grep -i -v "ion"
 ```
 
 ## Visualize the Kraken Reports with Pavian
@@ -252,7 +252,7 @@ Copy our already downloaded file.
 <!-- This was downloaded 11/8/2024 and took approximately 17 minutes-->
 
 ```{bash, eval=FALSE}
-cp /home/data/metagenomics-2310/centrifuge/eupath/eupathDB.tar.gz .
+cp /home/data/metagenomics/centrifuge/eupath/eupathDB.tar.gz .
 ```
 
 This is a compressed tarball file that contains several files. Let's uncompress it and look into the library file it created.

11-SqueezeMeta.Rmd

@@ -49,7 +49,7 @@ screen -S squeezemeta
 # Download from source and format the latest version of the annotation databases for use with SqueezeMeta.
 # Do not do this step for this tutorial (It took ~14 hours).
 
-make_databases.pl /home/$USER/squeezemeta/database
+make_databases.pl /home/<username>/squeezemeta/database
 ```
 
 ## Data Download
@@ -72,7 +72,7 @@ Or copy it from here: /home/data/metagenomics-2310/squeezemeta/SraRunTable.txt
 
 ```{bash, eval=FALSE}
 # Copy accessions list:
-cp /home/data/metagenomics-2310/squeezemeta/sra_ids.txt .
+cp /home/data/metagenomics/squeezemeta/sra_ids.txt .
 
 # Activate sra-tools environment:
 conda activate sra-tools
@@ -103,21 +103,21 @@ conda deactivate
 source activate squeezemeta
 
 # Create a symbolic link to fastq files if download didn't have time to finish
-cd /home/$USER/squeezemeta/fastq
-ln -s /home/elavelle/squeezemeta/fastq/new/*gz ./
+cd ~/squeezemeta/fastq
+ln -s /home/data/metagenomics/squeezemeta/fastq/new/*gz ./
 
 # This is an assembly based method of metatranscriptomics (Finished running in ~4.25 hours)
-cd /home/$USER/squeezemeta
+cd ~/squeezemeta
 SqueezeMeta.pl -m coassembly -p gingivitis_assembly_based -s sample_file.txt \
--f /home/$USER/squeezemeta/fastq -a megahit -map minimap2-sr
+-f /home/<username>/squeezemeta/fastq -a megahit -map minimap2-sr
 
 # This is read based method of metatranscriptomics (Finished running in ~48 hours)
 sqm_reads.pl -p gingivitis_read_based -s sample_file.txt \
--f /home/$USER/squeezemeta/fastq \
+-f /home/<username>/squeezemeta/fastq \
 --memory 0.1 --num-cpu-threads 12 --euk
 
 # Softlink to pre-run output directory
-ln -s /home/elavelle/squeezemeta/gingivitis_2 /home/$USER/squeezemeta/
+ln -s /home/data/metagenomics/squeezemeta/gingivitis_2 /home/<username>/squeezemeta/
 
 
 # Deactivate the environment and launch R
@@ -139,7 +139,7 @@ https://github.com/jtamames/SqueezeMeta/wiki/Using-R-to-analyze-your-SQM-results
 library('SQMtools')
 # set working directory to directory containing gingivitis_2 folder
 
-setwd('/home/$USER/squeezemeta/')
+setwd('/home/<username>/squeezemeta/')
 # Load SqueezeMeta data into R
 gingivitis = loadSQM('gingivitis_2')
 ```

index.Rmd

@@ -538,7 +538,7 @@ You should be returned to your prompt: username@metagenomics-2310:~/linuxc$
 #### Syntax: ln -s FileYouWantToLink/PointTo NameYouWantToGiveIt{-}
 
 ```{bash,eval=FALSE}
-ln -s /home/data/metagenomics-2310/covid.fasta covid.fasta
+ln -s /home/data/metagenomics/covid.fasta covid.fasta
 
 ls -l
 ```
@@ -636,7 +636,7 @@ cat covid.fasta | tail
 Fastq files contain sequence reads and associated **meta data**.
 
 ```{bash,eval=FALSE}
-ln -s /home/data/metagenomics-2310/SP1.fq 
+ln -s /home/data/metagenomics/SP1.fq 
 
 ls -ltr
 ```
@@ -838,7 +838,7 @@ Powerful Z commands (zcat)
 Let’s copy another file:
 
 ```{bash,eval=FALSE}
-cp /home/data/metagenomics-2310/table1.txt.gz .
+cp /home/data/metagenomics/table1.txt.gz .
 zcat table1.txt.gz
 
 ```