Where to find ERR samples information ?

Question

[XBria]

Hi, Please help me with finding the sample info like read length and platform used in ERR188337 for example ?

Thanks

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Answer 1

[Pierre Lindenbaum]

search SRA: https://www.ncbi.nlm.nih.gov/sra/?term=ERR188337

https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR188337

ILLUMINA (Illumina HiSeq 2000) , paired-end, 75 bp

[XBria]

Thank you :) very immediate help Can you please the above comment I made, and let me know where 75 bp is written ?

[Pierre Lindenbaum]

I've looked at the "Reads" tab in https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR188337

>gnl|SRA|ERR188337.1.1 HWI-ST661:131:C051TACXX:2:1101:1192:2142 (Biological)
NGGCGGACGAGAGTGAGACAGCAGTGAAGCCGCCGGCACCTCCGCTGCCGCAGATGATGG
AAGGGAACGGGAACN
>gnl|SRA|ERR188337.1.2 HWI-ST661:131:C051TACXX:2:1101:1192:2142 (Biological)
TGTCTCACTGCCTTTTTCTTTCTTCTTTTTTTGTTTCTTTTTCTTCTTTTTGGCTCCAGT
GTCATTGGCTGNNNN

[WouterDeCoster]

You realize you can just count the number of nucleotides to get the read length, right?

[XBria]

I 've read on wikipedia the first line of a fastq file contains read length, I can find the readlength in SRA though.

[GenoMax]

Not normally. SRA may include that as a post-processed result. They also change the original Illumina identifiers (though you can recover the originals by using -F option during fastq-dump).

Answer 2

[jared.andrews07]

You can always back-reference to the relevant ENA page, which usually contains the platform. You can usually infer the approximate read length from the platform. Or download it and run it through FastQC or the such. The ENA search function was how I found that page.

[XBria]

Dear Jared,

I open the fastq file and see the following:

@ERR188044.9 HWI-ST457:201:C0EWEACXX:1:1101:2976:1993/1
CAAGTTCTTTCCTTCCCTGCCAGCCAGATAGATAGACAGATGGGAAAGGCAGGCGCGGCCTTCGTTGTCAGTAGTT
+
CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJIIHDDAECD?CC@CDDCDC>>
@ERR188044.35 HWI-ST457:201:C0EWEACXX:1:1101:8799:1991/1
CCACTGCCGAGAATGCTAGGCTTCTGGCCCAGAAAAGAGGAGCTTTGCAGGGCTCTGCATGGCAGGTTAGCTCAGA
+
CCCFFFFFHGHGHIJJJIJJJJJJIIJJJJJJJJJJJJJJJIJJJIJFIJIIIIIJJHHHHHFFFD;>C@CCDDD@
@ERR188044.92 HWI-ST457:201:C0EWEACXX:1:1101:19896:1985/1
GGCGAATCGTAATGAGGCGTGCGCCGCCAATATGCACTGTACATTCCACAAGCATTGCCTTCTTATTTTACTTCTT
+
CCCFFFFFHHHHHJJJJIJEHGGGHIIJJJJIJJJJIJJHGHHHHHHGFFFFFEEEEEEDDDDDDDEEEEDDCCDA
@ERR188044.120 HWI-ST457:201:C0EWEACXX:1:1101:1538:2090/1
CGGCAGTGATCACACGTCGGCTGCTGGGAAGATCTGGATTCTCGTTTCAGGTCACCATCAGAAAAGCTAAGTTTGC
+

is the readlength 201 ? Am I right ?

[GenoMax]

Where do you see 201? It is 76 bp.