Skip to content

Original FastQ headers  #130

@hp2048

Description

@hp2048

Hi
We have downloaded SRA file from https://sra-download.ncbi.nlm.nih.gov/traces/era14/ERR/ERR1019/ERR1019069.

We are using prebuilt fastq-dump (v2.9.0) sratoolkit.2.9.0-centos_linux64/bin/fastq-dump.2.9.0.

The command to get FastQ files from the SRA file was as follows:

fastq-dump -v 1 --split-3 -F -X 3 -Z ERR1019069.sra

RESULT:

@1
GGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGGTTAGGGTTAGGGTTAGGGTTAGGGTT
+1
@@BDFFFBFFHFDEHHIGIFHFGIJCDCGHGBHHIHI?DFFHIFGFCHH=CHIIG.=AHHH;?D?C>6;;?CBBBB(5?#####################
@1
CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA
+1
CCCFFFFFHHHHHJJIIJIJJJGGGIHIJJJIGGIIJIFJJJJIJJJIFHGCGHJIEGGIHHGC@@BEDEEECDBD(=BD<<CB?A?<38A+293(88<<
@2
CCTAACCCTAACCCCTAACCCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCAACCCCTACCCCCTACCTCTAACCATAACCCTAACCCTAAC
+2
CCCFFFFFHHHHGJIGEGIGHH=H;EFDH7?BBFFC;3BDGHE3BGCCHHGII2@CHEH#########################################
@2
TAGGGTTGGGTTAGGGTTAGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGGTAGGGTTGGGTTAGGGGTAGGGTTAGGGTTAGGGTTGGGGGTAGGGTT
+2
@@@FFDDFHHHHHGEIEECHHH9EBFHI*8@FI6B=FCC=;CEGC)8(6@C#################################################
@3
GTTAGGGTTAGGGTTAGGGTTGGGTTAGGGTTGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTGTT
+3
@@@DFFFDFFDHHEGGHJJ@FHHI?F=FIJ@FHIE;;?BDGBC@GFH.=@@EEAHFBFF@CBACD;;?ACB(9<<<A>ABA?89???C?+8<A?A#####
@3
CTAACCCTAACCCTAACCCTAACCCTAACCCTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTACCCAAACCCCTAACCCCAAC
+3
CCCFFFFFHHHHHJJJJJJJIIIJIIJJJJICHIJJECHHIJ<FFGGH;CFHEG9FGGI9(=7AE?67)>@2655?########################

I have also used --defline-seq '$ac $si $sn $sg $ri $rn' with no avail in retrieving standard Illumina headers.

Could you please let us know how to get original headers like the following?

@HWUSI-EAS100R:6:73:941:1973#0/1

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions