I download SRR5376997.sra from NCBI
and i convert SRA to fastq using SRA toolkit
fastq-dump SRR5376997.sra
output: SRR5376997.fastq
head SRR5376997.fastq
@SRR5376997.1 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=202 TGTTAAATGATCTAATGAAAAAGATAAACAATTACATAAACAGATGGGGAATTTCAGAGAACTAAAAACTATTTTAAAAGAGTCAAAGAGAAATGCTAAAAC CTTTTTTCTTCTTGTGTTTCAGTTTAGATCGTCTCTATTGGAACATCTTTAAGTTCACTGATTCTTTCCTTAGCTGTGTCCAATCTGCTGATGAGCCTGT
+SRR5376997.1 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=202 @@BFFFFFGGHHH@GGHGIJJJJHGHIJJJJAFGEFCIEGGHIJEHIIJIBGHIHGGGIIIIJJJJJJJGGGIAGAHHHGFF@CDDAED@6>;@ACDDDDDCCCFFFFFDHFGHIG<ecgiggifiiehigijhijijdfiehghg@dghef@fhf>FEH@FFHHII@FGGG@EGIGEEHHGHFFFFCEECEEEEAAACCB>
@SRR5376997.2 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=202 GCTTTCTGGCATTTGCCGATGCCCCCTTCTCTCCCTCTGGGGGGTTTGTGTGTATAAGTGCGTGGGCAGGGAGGCCGCGGAGGCGGCGCCGCGGGCGCTCT GCTGAATTAAACGGTGTCCTGGTCTTCAAGGAGCTTACAAGTGAGAGCGCCCGCGGCGCCGCCTCCGCGGCCTCCCTGCCCACGCACTTATACACACAAAC
+SRR5376997.2 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=202 CCCFFFFFHHDHHJJJJJIJJIJJJJJJJIJHIJIGHHIGIJID5:BDACABADDEEDCCDDBBDDDDDDDBDDB?@DDDDDDD>B9<bdbd@@ddbb>B<bccfdfffhghhhjaffhhhijfhdhijijjhjjjjjjjjjghiiggghjdhgiigfdbdddddddddddbdbdddcdddd4<@b<@bccdddedcb?8?b< p="">
@SRR5376997.3 HWI-ST1215:350:C42MLACXX:8:1101:1963:2152 length=202 CCTTAAGAGGTATGAATGATTGTGATTTGGTGCTTTGGACAATGCCATGTAGAGTGCTTCTTTGGGGGTGAGGGATAGACAGACCCTAGGGGCTCTGAGCT GGAGGCACCTGAAGCTGCCTCTTCCTCCAAGTCAAGAGAATCCTTTCTCCCCATCTTCACAGTCTCACAGCTCACTTCATCTTCCCCGTCCTCACTTTCTT
Q1. how can i know this fastq is paired or not?
Q2. What is the meaning @SRR5376997.1 @SRR5376997.2 @SRR5376997.3???? what is meaning .1 .2 .3 ???
And i split paired end fastq using SRA toolkit(fastq-dump)
fastq-dump -I --split-files SRR5376997.sra
output: SRR5376997_1.fastq SRR5376997_2.fastq
head SRR5376997_1.fastq
@SRR5376997.1.1 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=101 TGTTAAATGATCTAATGAAAAAGATAAACAATTACATAAACAGATGGGGAATTTCAGAGAACTAAAAACTATTTTAAAAGAGTCAAAGAGAAATGCTAAAA
+SRR5376997.1.1 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=101 @@BFFFFFGGHHH@GGHGIJJJJHGHIJJJJAFGEFCIEGGHIJEHIIJIBGHIHGGGIIIIJJJJJJJGGGIAGAHHHGFF@CDDAED@6>;@ACDDDDD @SRR5376997.2.1 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=101 GCTTTCTGGCATTTGCCGATGCCCCCTTCTCTCCCTCTGGGGGGTTTGTGTGTATAAGTGCGTGGGCAGGGAGGCCGCGGAGGCGGCGCCGCGGGCGCTCT
+SRR5376997.2.1 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=101 CCCFFFFFHHDHHJJJJJIJJIJJJJJJJIJHIJIGHHIGIJID5:BDACABADDEEDCCDDBBDDDDDDDBDDB?@DDDDDDD>B9<bdbd@@ddbb>B< @SRR5376997.3.1 HWI-ST1215:350:C42MLACXX:8:1101:1963:2152 length=101 CCTTAAGAGGTATGAATGATTGTGATTTGGTGCTTTGGACAATGCCATGTAGAGTGCTTCTTTGGGGGTGAGGGATAGACAGACCCTAGGGGCTCTGAGCT
head SRR5376997_2.fastq
@SRR5376997.1.2 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=101 CCTTTTTTCTTCTTGTGTTTCAGTTTAGATCGTCTCTATTGGAACATCTTTAAGTTCACTGATTCTTTCCTTAGCTGTGTCCAATCTGCTGATGAGCCTGT +SRR5376997.1.2 HWI-ST1215:350:C42MLACXX:8:1101:1631:2122 length=101 CCCFFFFFDHFGHIG<ecgiggifiiehigijhijijdfiehghg@dghef@fhf>FEH@FFHHII@FGGG@EGIGEEHHGHFFFFCEECEEEEAAACCB>
@SRR5376997.2.2 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=101 GCTGAATTAAACGGTGTCCTGGTCTTCAAGGAGCTTACAAGTGAGAGCGCCCGCGGCGCCGCCTCCGCGGCCTCCCTGCCCACGCACTTATACACACAAAC+SRR5376997.2.2 HWI-ST1215:350:C42MLACXX:8:1101:1971:2133 length=101 BCCFDFFFHGHHHJAFFHHHIJFHDHIJIJJHJJJJJJJJJGHIIGGGHJDHGIIGFDBDDDDDDDDDDDBDBDDDCDDDD4<@B<@BCCDDDEDCB?8?B
@SRR5376997.3.2 HWI-ST1215:350:C42MLACXX:8:1101:1963:2152 length=101 GGAGGCACCTGAAGCTGCCTCTTCCTCCAAGTCAAGAGAATCCTTTCTCCCCATCTTCACAGTCTCACAGCTCACTTCATCTTCCCCGTCCTCACTTTCTT
As you can see above, SRR5376997.fastq -> SRR5376997_1.fastq(non-Bold) SRR5376997_2.fastq(Bold)
TGTTAAATGATCTAATGAAAAAGATAAACAATTACATAAACAGATGGGGAATTTCAGAGAACTAAAAACTATTTTAAAAGAGTCAAAGAGAAATGCTAAAA CCTTTTTTCTTCTTGTGTTTCAGTTTAGATCGTCTCTATTGGAACATCTTTAAGTTCACTGATTCTTTCCTTAGCTGTGTCCAATCTGCTGATGAGCCTGT
Q3. it means non-bold(SRR5376997_1) is paired with bold(SRR5376997_2)???
Q1. how can i know this fastq is paired or not?
Q2. What is the meaning @SRR5376997.1 @SRR5376997.2 @SRR5376997.3???? what is meaning .1 .2 .3 ???
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2 answers
When in doubt check EBI-ENA for downloading fastq files. SRR5376997 is indeed a paired-end data set.
What is the meaning @SRR5376997.1 @SRR5376997.2 @SRR5376997.3???? what is meaning .1 .2 .3 ???
*.1, *.2, *.3 is just sequential read numbering. If you use fastq-dump with -F option you should recover original Illumina format headers without the SRR* accession numbers.
You find the information of paired-end sequencing in the study information : https://www.ncbi.nlm.nih.gov/sra/SRX2672295
Layout: PAIRED
In Illumina documentation R1 is forward and R2 is reverse (depends on your sequencing kit) https://emea.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf
If you do not --split-files in your fastq-dump command, both forward and reverse reads are mixed in your file SRR5376997.fastq
Reads in R2 file are reverse complement to be from 5' to 3' in your fastq file so you have the following :
#R1 :
ATGC
#R2:
GTCA
#Result
ATGC----->
<-----TGAC
In any case I go to ENA to download these SRR files
You can use this tuto to download your files : Fast download of FASTQ files from the European Nucleotide Archive (ENA)
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