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SRA to fastq

The command used to convert sra to fastq is fastq-dump --split-3 ERR738423.sra The above sra is single-end data. SRA file size is 2.2GB; using fastq-dump command fastq file obtained is 10.2GB; in ENA fastq file is 7GB. Why there is a huge difference in size?

rna-seq
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updated by Satyajeet Khare Satyajeet Khare • written by vimlakany • vimlakany

2 answers

Hi,

ENA files are smaller that GEO because in line 3 '+' character is not followed by the sequence identifier. For example, in GEO it is

@ENTIRE_SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+ENTIRE_SEQ_ID
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

But in ENA it is

@ENTIRE_SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

At least, that was the case with my datasets.

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written by Satyajeet Khare Satyajeet Khare

But this problem exits in SRA to fastq also.

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written by vimlakany • vimlakany

Yes. I mean it depends on the source of SRA file. Can you 'head' both fastq files and check if there is difference in line 3?

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written by Satyajeet Khare Satyajeet Khare

Check the content:

  1. Sequence number:

    grep -c '^' reads.fastq

  2. Sequence header line format:

    grep '^' reads.fastq | head -n 10
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written by shenwei356 shenwei356

Sequence number: 168124864

Sequence header line @ERR738423.1 HWI-ST365_0182:2:1101:1134:2086#CGATGT length=50 AGTGTCTAAGGGCGCATGGTGGATGCCTTGGCATCGAGAGCCGATGAAGG +ERR738423.1 HWI-ST365_0182:2:1101:1134:2086#CGATGT length=50 @@=D?DDD?DDF1C1FHIGE@GGHGEHHGEIC>B>FHH?AGC>AFHCHGG @ERR738423.2 HWI-ST365_0182:2:1101:1152:2089#CGATGT length=50 CCGAACCCGGAAGCTAAGCCTGCCAGCGCCGATGATACTGCCCCTCCGGG +ERR738423.2 HWI-ST365_0182:2:1101:1152:2089#CGATGT length=50 CCCFFFFFHHGHHJJIIIIJJJJJIJIJIJJGHIJJJJIIIJJFHHFFDD @ERR738423.3 HWI-ST365_0182:2:1101:1095:2121#CGATGT length=50 TCAAGCACACCGCCGAAGCCGCGGCACATCCACCTTGTGGTGGGAGTGGG

Why should we check sequence number and sequence header line format?

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written by vimlakany • vimlakany

i mean compare these infomation between the two files.

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written by shenwei356 shenwei356

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