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Examples.md

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Examples of using iSeq

Basic examples

  1. Download all Run sequencing data and metadata associated with a Project

    iseq -i PRJNA211801

    e01

    if you run the same code again, iSeq will skip downloaded data

    e01_1

    iseq -i CRA000553

    iSeq will prioritize access to the HUAWEI Cloud when accessing the GSA database.

    e02

    iseq -i GSE122139

    If the MD5 check fails after the sequencing data is downloaded, iSeq will attempt to re-download up to 3 times. If it still fails, the ID will be stored in the fail.log file.

    e03

    iseq -i SRR931847 -o PRJNA211801

    iSeq will save result in PRJNA211801 directory.

    e13

  2. Download all sequencing data and metadata associated with an Experiment or a BioSample

    iseq -i SRX477044
iseq -i CRX020217
iseq -i GSM7417667

  3. Download a single sequencing data and metadata associated with a Run

    iseq -i SRR1178105
iseq -i CRR311377

  4. Only download metadata information

    iseq -i PRJNA211801 -m

    e04

  5. Download SRA files and convert them to FASTQ files

    iseq -i SRR1178105 -q

    e05

  6. Download sequencing data in parallel with 10 connections

    iseq -i SRR1178105 -p 10

    e06

  7. Download sequencing data by Aspera

    iseq -i SRR1178105 -a

    e07

    iseq -i CRR311377 -a

    When accessing the GSA database using Aspera, it will still prioritize access to the HUAWEI Cloud. If it is not available, it will proceed with the normal download using Aspera

    e07_1

  8. Download gzip-formatted FASTQ files directly

    iseq -i SRR1178105 -g

    e08

  9. Merge multiple FASTQ files into one FASTQ file

    • Merge multiple FASTQ files into one FASTQ file for each Experiment.
    iseq -i CRX020217 -e ex

    e09

    • Merge multiple FASTQ files into one FASTQ file for each Sample.
    rm success.log
iseq -i SAMC017083 -e sa

    e09

    • Merge multiple FASTQ files into one FASTQ file for each Study.
     rm success.log
 iseq -i PRJCA000613 -e st

    e09

  10. Download sequencing data from SRA database

     iseq -i SRR1178105 -d sra

    e10

Advanced examples

  1. Use 10 connections to download SRA files in parallel with -p 10, then demultiplex into FASTQ files with the default 8 threads using -q and quickly compress with -g. Finally, merge Runs from the same Experiment with -e.

    iseq -i SRX2993509 -q -g -p 10 -e ex

    e11

  2. Use Aspera with -a to directly download gzip-formatted FASTQ files with -g, and then merge Runs from the same Experiment. If there is only one Run, rename it with -e.

    iseq -i PRJNA211801 -a -g -e ex

    e12

  3. Batch download by giving a file and using Aspera with -a to directly download gzip-formatted FASTQ files with -g.

    iseq -i SRR_Acc_List.txt -a -g

    e13