Merge pull request #139 from AlexsLemonade/sjspielman/update-fastq-su…

…bset Update fastq subset files
AlexsLemonade · Oct 20, 2023 · 730de1d · 730de1d
2 parents 591b039 + 54aa8f6
commit 730de1d
Show file tree

Hide file tree

Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/instructor_notes/fastq_subset/README.md b/instructor_notes/fastq_subset/README.md
@@ -1,3 +1,3 @@
-These FASTQ files are subsetted versions (to only the first 10,000 reads) of the full files here: https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP255885
+These FASTQ files are subsetted versions (to only the first 10,000 reads) of two of the samples from this project: https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP255885.
 
-These files are obtained and processed with `generate_fastq_subsets.sh`, and they can be used as alternative FASTQ files to download when internet speed is prohibitive.
+Files are obtained from EBI and processed with `generate_fastq_subsets.sh`, and they can be used as alternative FASTQ files to download when internet speed is prohibitive.
diff --git a/instructor_notes/fastq_subset/generate_fastq_subsets.sh b/instructor_notes/fastq_subset/generate_fastq_subsets.sh
@@ -9,7 +9,7 @@ set -euo pipefail
 # Provide a single argument: the FASTQ name, without `.gz` extension
 function subset_fastq() {
     # Grab the file
-    curl -sO https://sra-download.ncbi.nlm.nih.gov/traces/sra63/SRZ/011518/SRR11518889/$1.gz
+    curl -sO ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR115/089/SRR11518889/$1.gz
 
     # Unzip and take first 10000 records (40000 lines)
     gunzip -fc $1.gz \
@@ -24,6 +24,6 @@ function subset_fastq() {
 }
 
 
-subset_fastq "NC16_S1_L004_R1_001.fastq"
-subset_fastq "NC16_S1_L004_R2_001.fastq"
+subset_fastq "SRR11518889_1.fastq"
+subset_fastq "SRR11518889_2.fastq"
 
diff --git a/...ubset/subset-NC16_S1_L004_R1_001.fastq.gz → ...astq_subset/subset-SRR11518889_1.fastq.gz b/...ubset/subset-NC16_S1_L004_R1_001.fastq.gz → ...astq_subset/subset-SRR11518889_1.fastq.gz
diff --git a/...ubset/subset-NC16_S1_L004_R2_001.fastq.gz → ...astq_subset/subset-SRR11518889_2.fastq.gz b/...ubset/subset-NC16_S1_L004_R2_001.fastq.gz → ...astq_subset/subset-SRR11518889_2.fastq.gz