diff --git a/instructor_notes/fastq_subset/README.md b/instructor_notes/fastq_subset/README.md index c96ec02..43eb751 100644 --- 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 index eb87dc4..a006d30 100644 --- 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/instructor_notes/fastq_subset/subset-NC16_S1_L004_R1_001.fastq.gz b/instructor_notes/fastq_subset/subset-SRR11518889_1.fastq.gz similarity index 100% rename from instructor_notes/fastq_subset/subset-NC16_S1_L004_R1_001.fastq.gz rename to instructor_notes/fastq_subset/subset-SRR11518889_1.fastq.gz diff --git a/instructor_notes/fastq_subset/subset-NC16_S1_L004_R2_001.fastq.gz b/instructor_notes/fastq_subset/subset-SRR11518889_2.fastq.gz similarity index 100% rename from instructor_notes/fastq_subset/subset-NC16_S1_L004_R2_001.fastq.gz rename to instructor_notes/fastq_subset/subset-SRR11518889_2.fastq.gz