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Forum: Bioinformatics 04-20-2018, 08:00 AM
Replies: 1
Views: 763
Posted By Liam_Gallagher
Check this:...

Check this: http://ab.inf.uni-tuebingen.de/software/megan6/
It uses DIAMOND to align sequences, then MEGAN for the taxonomic analysis.
Hope it helps!
Forum: Bioinformatics 04-20-2018, 07:26 AM
Replies: 0
Views: 394
Posted By Liam_Gallagher
Cool Question on reads mapping smallRNA-seq (100% feature coverage)

Hi all,
I have a fastq file containing reads from an Illumina NextSeq smallRNA sequencing, a fasta file representing the genome (it is composed by about 33000 sequences with length 18-35 nts), the...
Forum: Bioinformatics 10-27-2017, 05:02 AM
Replies: 0
Views: 522
Posted By Liam_Gallagher
Lightbulb Help in output only the alignments identical to the reference

Hello everyone,
I have a SAM file resulting from a STAR alignment, containing reads aligned to a reference of smallRNA sequences (I created the reference, downloading the fasta sequences of interest...
Forum: Bioinformatics 11-25-2013, 02:41 AM
Replies: 5
Views: 5,560
Posted By Liam_Gallagher
If you have the VCF file, you can also use...

If you have the VCF file, you can also use wAnnovar: http://wannovar.usc.edu/
Forum: Bioinformatics 10-22-2013, 02:17 AM
Replies: 6
Views: 3,413
Posted By Liam_Gallagher
Wow! You gave me a lot of informations, m_two and...

Wow! You gave me a lot of informations, m_two and plattsa! thank you!!
Forum: Bioinformatics 10-14-2013, 07:30 AM
Replies: 6
Views: 3,413
Posted By Liam_Gallagher
VCF to disease-causing variants

Hello,
I have a list of variations in VCF format and I would like to find if some of these are known disease-causing variants. I'm looking for a tool with which I can upload (or set as input) my VCF...
Forum: Bioinformatics 02-16-2013, 01:05 AM
Replies: 4
Views: 999
Posted By Liam_Gallagher
Hmm....I would try to use the WT (assembled...

Hmm....I would try to use the WT (assembled de-novo) as reference for aligning the mutant and then use a variant caller, to identify variants between two genomes (using the WT as reference).

Also...
Forum: Bioinformatics 02-12-2013, 10:20 AM
Replies: 5
Views: 1,621
Posted By Liam_Gallagher
Thank you very much for your suggestions....they...

Thank you very much for your suggestions....they are very helpful!! :)
Forum: Bioinformatics 02-11-2013, 10:25 AM
Replies: 5
Views: 1,621
Posted By Liam_Gallagher
Yes...I know about summarize_annovar, but I was...

Yes...I know about summarize_annovar, but I was not able to get it working...because of an error. Today I tried to redownload some database, and now it works fine!
Fortunately I have just some...
Forum: Bioinformatics 02-10-2013, 07:44 AM
Replies: 5
Views: 1,621
Posted By Liam_Gallagher
Combine annotations

Hi all...could you suggest me a way to combine annotations coming from different files and related to the same subject (e.g. the same genomic coordinate) ? I was thinking about Annovar (tool to...
Forum: Bioinformatics 05-10-2012, 02:34 AM
Replies: 5
Views: 6,339
Posted By Liam_Gallagher
Unfortunataly Blat requires in input the amino...

Unfortunataly Blat requires in input the amino acidic sequence....but I only have the position of the mutated AA. I know how to get the AA sequence but I was looking for an automatic method...any...
Forum: Sample Prep / Library Generation 05-10-2012, 02:15 AM
Replies: 1
Views: 1,120
Posted By Liam_Gallagher
Yes...it is the same release that we use (for...

Yes...it is the same release that we use (for High Sensitivity DNA chip).
Write down your license keys before upgrading....in case you need for activating the new release (in 2100 bioanalyzer...
Forum: Bioinformatics 05-09-2012, 04:50 AM
Replies: 5
Views: 6,339
Posted By Liam_Gallagher
Thanks Richard for the quick reply! ahah I...

Thanks Richard for the quick reply!
ahah I think Blat is gonna be the tool who saves me...and after all will be my Wonderwall! :-) hope you like Oasis.... :-)
Thank you very much, i will try!!
Forum: Bioinformatics 05-08-2012, 07:29 AM
Replies: 5
Views: 6,339
Posted By Liam_Gallagher
I know that some tools (e.g. Ensembl Variant...

I know that some tools (e.g. Ensembl Variant Effect Predictor..) can predict the effect of a DNA mutation (providing in input a list of genomic coordinates of the variants) on transcripts and...
Forum: Bioinformatics 05-08-2012, 07:16 AM
Replies: 5
Views: 6,339
Posted By Liam_Gallagher
cDNA or protein location to genomic DNA location

Hi all,

I have a list of protein mutations and cDNA mutations and I would like to obtain the original genomic locations. Is there a tool to convert the location from cDNA or protein (maybe...
Forum: Ion Torrent 11-10-2011, 12:47 AM
Replies: 8
Views: 4,524
Posted By Liam_Gallagher
Thank you all! We just bought the same one...

Thank you all!
We just bought the same one suggested by ptran.
It also should be compatible with the SW module that shutdown the server if the power goes out.

Cristian
Forum: Ion Torrent 10-21-2011, 12:05 AM
Replies: 8
Views: 4,524
Posted By Liam_Gallagher
Thank you Phillip! Yes, we alredy have the...

Thank you Phillip!
Yes, we alredy have the "Site Preparation Guide" form Life Technologies...but in this user manual it is only specified that an UPS (from Multiple Suppliers) is required and should...
Forum: Ion Torrent 10-20-2011, 07:14 AM
Replies: 8
Views: 4,524
Posted By Liam_Gallagher
UPS (Uninterruptible Power Supply) with Ion Torrent

Hi all!
Does anyone of you use an UPS for preventing power failures ? If yes...which one do you use ?
I'm preparing the lab for the installation of the Ion Torrent PGM and Torrent Server and I...
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