Question: Transform smallRNA SRA (Illumina) sequences to FASTA
0
gravatar for juanma_lace
5.0 years ago by
juanma_lace20
Argentina
juanma_lace20 wrote:

Hi all,

I'm running an analysis of small RNA and I want to use some libs from NCBI in SRA (Illumina).

The problem is that all the reads are 35 bp long (I understand they have some kind of adaptors).

I want to know how to obtain the real fasta sequences programatically (I want to use them in a pipeline)

thank you in advance

Seqs files:

http://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=241290

sra adaptor smallrna illumina fasta • 1.6k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 5.0 years ago by juanma_lace20
0
gravatar for RamRS
5.0 years ago by
RamRS25k
Houston, TX
RamRS25k wrote:

The SRA toolkit should help you: http://www.ncbi.nlm.nih.gov/sites/books/NBK158900/

ADD COMMENTlink written 5.0 years ago by RamRS25k

I see that illumina-dump creates a lot of files, how can I get the fasta from those files

ADD REPLYlink written 5.0 years ago by juanma_lace20

Here you go. But seriously, this stuff is harder to find than it needs to be:

fastq-dump SRR1196045 --split-spot --fasta
ADD REPLYlink written 5.0 years ago by Matt Shirley9.2k

thank you for the sarcasm, anyway it does not answer my question. My question is about removing the adaptors, not just converting. 

ADD REPLYlink written 5.0 years ago by juanma_lace20
1

I'm sorry for the sarcasm - I think it's the first time I've used that site, and I agree now that it seems overly harsh. RamRS's link suggests cutadapt, which should trim any adapter sequence you specify. The hard part is finding the correct adapter sequence to trim, and FastQC might help you with that.

ADD REPLYlink written 5.0 years ago by Matt Shirley9.2k

cutadapt, fastqc and trimmomatic might help with trimming adapters.

EDIT: Lorena Pantano has given a much better, detailed response here: C: Transform smallRNA SRA (Illumina) sequences to FASTA

And yes, lmgtfy can be a bit too condescending at times. I think the cultural difference amplifies the effect, unfortunately.

ADD REPLYlink modified 4.9 years ago • written 5.0 years ago by RamRS25k
2

there are some adapter removal that are specific for mRNA and not small RNA. I would use cutadapt. The adapter in smallRNA is always the same, and it is enough to detect 8 nucleotides. The adapter should be something like AGATCGGAAGAGCAC, or without the first A if it is standard protocol. Fastqc was not working well the last time I used it (1/2 years ago, and the author admitted it was not prepare for small RNA).

ADD REPLYlink written 4.9 years ago by Lorena Pantano360

Thank you for the detailed response. It is better for the OP to hear from someone that shares research domain.

ADD REPLYlink written 4.9 years ago by RamRS25k

Does this help: http://www.ark-genomics.org/events-online-training-eu-training-course/adapter-and-quality-trimming-illumina-data

I don't have any XP with primer/adapter trimming :(

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by RamRS25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1898 users visited in the last hour