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Search: Posts Made By: slny
Forum: General 06-21-2020, 01:18 PM
Replies: 0
Views: 786
Posted By slny
Error in VCF annotation with Gvanno

Below is the command I used to run Gvanno:
./gvanno-1.3.0/gvanno.py ./sample.hard.filtered.vcf.gz --container docker ./gvanno-1.3.0 ./gvanno-1.3.0/examples grch37 ./gvanno-1.3.0/gvanno.toml out
...
Forum: Bioinformatics 03-03-2015, 08:04 AM
Replies: 7
Views: 1,695
Posted By slny
For Exome Seq data analysis, which instance...

For Exome Seq data analysis, which instance should I use?

Is there any way to increase 5 GB storage to 30 GB in EC2? After the usage, can I change the storage size back to 5 GB?
Forum: Bioinformatics 03-03-2015, 08:01 AM
Replies: 7
Views: 1,695
Posted By slny
Very useful links, thanks!

Very useful links, thanks!
Forum: Bioinformatics 03-02-2015, 09:40 PM
Replies: 7
Views: 1,695
Posted By slny
After I setup an instance, can I make change to...

After I setup an instance, can I make change to another instance if I find the chosen instance is not what I want?
Forum: Bioinformatics 02-27-2015, 09:44 AM
Replies: 7
Views: 1,695
Posted By slny
Thanks a lot! I will read this paper.

Thanks a lot! I will read this paper.
Forum: Bioinformatics 02-26-2015, 07:19 AM
Replies: 7
Views: 1,695
Posted By slny
Amazon Cloud question

I just created an Amazon Cloud account for NGS data analysis, but don't know how to set it up.

What's the instance that has NGS data analysis tools pre-installed?

Is there any good tutorial...
Forum: Bioinformatics 04-07-2013, 02:05 PM
Replies: 2
Views: 2,276
Posted By slny
CHIP-Seq analysis

I'm very new in ChIP Seq data analysis.

Is there any CHIP Seq analysis pipeline that I can use? Any tutorial of CHIP Seq data analysis?

Thanks,
Slny
Forum: Bioinformatics 10-13-2012, 08:57 AM
Replies: 7
Views: 2,940
Posted By slny
Hi Everyone, Thank you very much for all the...

Hi Everyone,

Thank you very much for all the responses. The information is very complete. I sincerely appreciate all the help!

Best,
slny
Forum: Bioinformatics 10-07-2012, 05:05 PM
Replies: 7
Views: 2,940
Posted By slny
commercial software in sequencing analysis

Hi,

I just got some funding to purchase commercial software for next generation sequencing data analysis, but I'm very new in sequencing analysis.

Could anyone give me a list of the commonly...
Forum: Bioinformatics 06-14-2011, 06:15 AM
Replies: 14
Views: 4,418
Posted By slny
Thanks a lot, steven.

Thanks a lot, steven.
Forum: Bioinformatics 06-08-2011, 12:31 PM
Replies: 0
Views: 1,565
Posted By slny
RepeatMasker question

Hi,

Under what circumstances should I use RepeatMasker to pre-process the sequencing data?

Thanks,
Slny
Forum: Bioinformatics 06-08-2011, 11:35 AM
Replies: 0
Views: 935
Posted By slny
contamination removal question

Hi,

I'm trying to remove contamination from the trimmed reads. Should I blast the reads against the contamination species genome or run sequence alignment against the contamination species...
Forum: Bioinformatics 06-08-2011, 11:32 AM
Replies: 14
Views: 4,418
Posted By slny
Thanks a lot for all the responses. The...

Thanks a lot for all the responses. The suggestions helped me a lot.
Forum: Bioinformatics 06-08-2011, 07:44 AM
Replies: 14
Views: 4,418
Posted By slny
steven, can SeqTrim take fastq file as input...

steven, can SeqTrim take fastq file as input files? I didn't find any input option for fastq format.
Forum: Bioinformatics 06-07-2011, 06:29 AM
Replies: 14
Views: 4,418
Posted By slny
Thanks, volks. It's a very useful tool for small...

Thanks, volks. It's a very useful tool for small non-coding RNA studies.
Forum: Bioinformatics 06-07-2011, 03:06 AM
Replies: 8
Views: 3,716
Posted By slny
Got it. Thanks a lot for all the helps.

Got it. Thanks a lot for all the helps.
Forum: Bioinformatics 06-07-2011, 03:04 AM
Replies: 14
Views: 4,418
Posted By slny
Thanks a lot. It's a very good paper.

Thanks a lot. It's a very good paper.
Forum: Bioinformatics 06-06-2011, 05:34 PM
Replies: 8
Views: 3,716
Posted By slny
Does removal of PCR duplicates mean that all the...

Does removal of PCR duplicates mean that all the reads are removed or only one read is kept?

If only one read is kept, then it won't influence the de novo assembling result no matter removing...
Forum: Bioinformatics 06-06-2011, 06:53 AM
Replies: 8
Views: 3,716
Posted By slny
For mRNA Seq, if we remove the PCR duplicates,...

For mRNA Seq, if we remove the PCR duplicates, which actually occurred by random chance, then we will get wrong read counts. Is removal of PCR duplicates also recommended in mRNA Seq?
Forum: Bioinformatics 06-06-2011, 06:19 AM
Replies: 9
Views: 3,301
Posted By slny
Got it. Thanks a lot!

Got it. Thanks a lot!
Forum: Bioinformatics 06-05-2011, 06:43 PM
Replies: 0
Views: 1,336
Posted By slny
ribosome DNA alignment question

Hi Everyone,

Should I align ribosome DNA before mRNA Seq analysis?

Thanks,
Slny
Forum: Bioinformatics 06-05-2011, 06:03 PM
Replies: 9
Views: 3,301
Posted By slny
Thanks a lot for your explanation. If I choose...

Thanks a lot for your explanation. If I choose bowtie for sequence alignment, should I run everything in TopHat because it also calls Bowtie? If so, I don't need to run a separate Bowtie before I...
Forum: Bioinformatics 06-05-2011, 04:46 PM
Replies: 8
Views: 3,716
Posted By slny
PCR duplicates questions

Hi,

I'm still confused about PCR duplicates removal and have some questions about it.

1. What is PCR duplicates? Can I say that all reads mapped to the same genome location are PCR...
Forum: Bioinformatics 06-05-2011, 03:24 PM
Replies: 9
Views: 3,301
Posted By slny
Thanks a lot for all the responses. Very...

Thanks a lot for all the responses. Very helpful.

pbluescript, do you use BWA for sequence alignments, and then re-align the unmapped reads with Bowtie followed with TopHat for exon junctions? ...
Forum: Bioinformatics 06-05-2011, 03:30 AM
Replies: 14
Views: 4,418
Posted By slny
Very good explanation. Thanks.

Very good explanation. Thanks.
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