Question: snp detection for sra files
gravatar for mailmeshain
2.1 years ago by
mailmeshain0 wrote:

hello i need an urgent help

i want to detect snp for sra files i did bwa and convert the file into bam format after that i have perform generate pileup data and i did varscan detection. after that which tool i have to select for snp please tell me the tools detail and thier small explanation


bwa snp galaxy • 581 views
ADD COMMENTlink modified 2.0 years ago • written 2.1 years ago by mailmeshain0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Tools in the groups NGS: VCF Manipulation and NGS: Variant Analysis can help with downstream data reduction for this type of analysis.

Specific help per tool can be found on each tool form itself. Many are also public and have links to the external documentation. General help and links to tutorials can be found at the top of this wiki:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k

hi dear i need your help i need to perform compartive analysis for vcf files. guide me how to perform it and i can compare files like for paried only or i can compare single or paired togther.


asap urgent

ADD REPLYlink written 2.0 years ago by mailmeshain0
gravatar for mailmeshain
2.0 years ago by
mailmeshain0 wrote:

thanku dear for the reply but right now i am performing the pipeline for snp detection from the galaxy tutorial. i have a question that my seq quality reads are not good for that i need your help regarding the trimming is the fastq qaulity trimmer sliding window for the good quality reads.

regards shwatank

ADD COMMENTlink written 2.0 years ago by mailmeshain0

Yes, this tool would be appropriate. If the results are not quite what you want, there are a few trimming tools in the same tool group. Perhaps try a few, compare, then decide which does the best job on your specific dataset.

Running FastQC after each, followed by mapping, to compare outputs is one option. The goal is to remove lower quality data but preserve as much sequence as possible, to maximise mapping rates (if the data is paired-end, concordant alignments is a key metric).

ADD REPLYlink written 2.0 years ago by Jennifer Hillman Jackson25k
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