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Update fastq subset files #139

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Oct 20, 2023
Merged

Update fastq subset files #139

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4 changes: 2 additions & 2 deletions instructor_notes/fastq_subset/README.md
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@@ -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.
6 changes: 3 additions & 3 deletions instructor_notes/fastq_subset/generate_fastq_subsets.sh
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Expand Up @@ -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 \
Expand All @@ -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"

0 ...ubset/subset-NC16_S1_L004_R1_001.fastq.gz → ...astq_subset/subset-SRR11518889_1.fastq.gz
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0 ...ubset/subset-NC16_S1_L004_R2_001.fastq.gz → ...astq_subset/subset-SRR11518889_2.fastq.gz
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File renamed without changes.