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  • GenoMax
    replied
    Originally posted by VC87 View Post
    Thanks again.By the way, do you know if it is possible to convert wig to fasta (or SRA)?
    https://www.biostars.org/p/48165/
    http://seqanswers.com/forums/showthread.php?t=21347

    SRA Format is only for their internal use.

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  • VC87
    replied
    Thanks again.By the way, do you know if it is possible to convert wig to fasta (or SRA)?

    Leave a comment:


  • GenoMax
    replied
    SRAtoolkit makes it easy to download the actual fastq data since you would have to uncompress the SRA files locally anyway. The toolkit saves you a step. You are most likely going to use the "fastq-dump" program. Help here: http://www.ncbi.nlm.nih.gov/Traces/s...ew=toolkit_doc

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  • VC87
    replied
    SRA, for now

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  • GenoMax
    replied
    Do you want the SRA files or the fastq files?

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  • VC87
    replied
    Does anyone know how to get the raw SRA files associated with the samples that we can search in the browser from the epigenomics database of NCBI? i suppose it should be possible to gte them from the sample ID but i dont know how to...

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  • VC87
    replied
    Genomax thanks for your reply!i'll check that out

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  • GenoMax
    replied
    A search found this: http://sra.dbcls.jp/search

    Project here: https://github.com/inutano/soylatte

    R-solution: https://www.bioconductor.org/package...tml/SRAdb.html

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  • VC87
    replied
    Yes i have.I want to search all SRA files from Bisulfite seq library fixing certain features such as organism, tissue, age, sex etc..thanks anyway for your reply!

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  • GenoMax
    replied
    Originally posted by VC87 View Post
    Hi!can someonde tell me how can i search SRA files trouhgh metadata features (wether in GEO, ENA..)?thanks in advance!
    Not sure what exactly you are looking for but have you tried the advanced search: http://www.ncbi.nlm.nih.gov/sra/advanced

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  • VC87
    replied
    Hi!can someonde tell me how can i search SRA files trouhgh metadata features (wether in GEO, ENA..)?thanks in advance!

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  • vadim
    replied
    Originally posted by dvanic View Post
    Hi! I've actually got the same question, albeit for a different dataset. If SRR123456_1.fastq mates with SRR123456_2.fastq, then what is the (much smaller), but still "properly" formatted and reasonably sized (~25 Mb in my case) SRR123456.fastq file???
    Thanks in advance!
    I believe SRR123456.fastq contains the "leftovers": reads with missing mates (due to filtering etc. )

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  • dvanic
    replied
    SRR016027_1.fastq.gz mates to SRR016027_2.fastq.gz, how about SRR016027.fastq.gz?
    Hi! I've actually got the same question, albeit for a different dataset. If SRR123456_1.fastq mates with SRR123456_2.fastq, then what is the (much smaller), but still "properly" formatted and reasonably sized (~25 Mb in my case) SRR123456.fastq file???
    Thanks in advance!

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  • bair
    replied
    Thank you, krobison

    That information is quite helpful.

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  • krobison
    replied
    This link may be helpful to you (it really should be featured more prominently on the SRA)
    http://www.ncbi.nlm.nih.gov/bookshel...cbi&part=Aug09

    Excerpt (I've added linebreaks for clarity). One might think that in your case each Experiment had different instrument parameters or library characteristics and somewhere it would be documented, but as far as I can tell these were all 80x1 runs. Wierd.
    An Experiment describes specifically what was sequenced and the method used. It includes information about the source of the DNA, the Sample, the sequencing platform, and the processing of the data.

    Each Experiment is made up of one or more instrument Runs.

    A Run contains the results or reads from each spot in the instrument run.

    In the future, some data will also have an associated Analysis. These Analyses may include assemblies of the short reads into genomic or transcript contigs and alignment to existing genomes or alignments with SRA data.

    Records at each level have unique accession identifiers with a specific three letter prefix that indicates the type of record: ERP or SRP for Studies, SRS for samples, SRX for Experiments, and SRR for Runs.

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