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Search: Posts Made By: Melissa
Forum: General 07-20-2018, 06:52 AM
Replies: 1
Views: 871
Posted By Melissa
What is the purpose of the computer besides...

What is the purpose of the computer besides storage? To perform bioinformatics analysis, I would want to have at least 10Tb hard disk, 64 CPUs and 120Gb of RAM.
Forum: General 04-09-2018, 02:13 AM
Replies: 1
Views: 1,288
Posted By Melissa
Ka/Ks calculation is a pair-wise comparison. It...

Ka/Ks calculation is a pair-wise comparison. It can be used for 2 purposes: 1) Comparison of orthologs between 2 different species; 2) Comparison of paralogs within a species to study...
Forum: Bioinformatics 05-09-2017, 05:05 AM
Replies: 1
Views: 702
Posted By Melissa
Thanks for the info. Good to know.

Thanks for the info. Good to know.
Forum: Bioinformatics 08-02-2016, 07:02 AM
Replies: 2
Views: 1,052
Posted By Melissa
It's always a problem getting primary transcript...

It's always a problem getting primary transcript without genome annotation. I'll probably use bedtools merge to merge all the transcripts into one long transcript and then use bedtools intersect to...
Forum: Bioinformatics 08-02-2016, 06:55 AM
Replies: 1
Views: 874
Posted By Melissa
SynMap seems to have E.coli genome. It will give...

SynMap seems to have E.coli genome. It will give you a dotplot and you can download the output files such as DAGchainer output files.

https://genomevolution.org/coge/SynMap.pl
Forum: Bioinformatics 07-15-2016, 04:51 AM
Replies: 6
Views: 1,121
Posted By Melissa
I agree with previous comments that ~20bp miRNA...

I agree with previous comments that ~20bp miRNA will not be sequenced. However, you can find primary miRNA transcripts in your transcriptomes because they are polyadenylated. Just download the...
Forum: Introductions 10-13-2015, 11:42 AM
Replies: 1
Views: 611
Posted By Melissa
Welcome! :)

Welcome! :)
Forum: General 05-08-2015, 12:10 PM
Replies: 5
Views: 1,967
Posted By Melissa
Will be nice to block all posts not written in...

Will be nice to block all posts not written in English. I've been irritated by non-English threads especially job postings despite the fact that google translate works very well nowadays. This kind...
Forum: Bioinformatics 05-06-2015, 10:37 PM
Replies: 9
Views: 1,098
Posted By Melissa
Hmm... I'm curious if there is such a list. A...

Hmm... I'm curious if there is such a list. A lowly expressed gene is either not activated or repressed. I think some people are overly concern about not getting sufficient depth of lowly expressed...
Forum: General 05-05-2015, 04:10 PM
Replies: 12
Views: 2,507
Posted By Melissa
Agree with Richard Finney. It's not like I can...

Agree with Richard Finney. It's not like I can put the ratings in my CV. I'm guessing most members are more interested in getting their problems solved.

I second the post tagging. I suggest...
Forum: Epigenetics 04-08-2015, 09:50 AM
Replies: 3
Views: 1,705
Posted By Melissa
Thanks for the info :)

Thanks for the info :)
Forum: Epigenetics 02-12-2015, 10:03 AM
Replies: 3
Views: 1,705
Posted By Melissa
I emailed Illumina tech support and the answer I...

I emailed Illumina tech support and the answer I got is rather vague. 200-800bp is recommended because it can be hard to sonicate ChIP dna to a smaller size. Seems like there is nothing wrong with...
Forum: Epigenetics 02-04-2015, 01:55 PM
Replies: 3
Views: 1,705
Posted By Melissa
Question Why sonicate DNA to 200-800bp?

Hi guys,

I don't understand why Illumina recommends an insert size of 200-800bp for Truseq ChIP library preparation when the protocol selects only 250-300 bp fragments for sequencing. Since...
Forum: Bioinformatics 01-23-2015, 01:17 PM
Replies: 1
Views: 762
Posted By Melissa
I'll either search against a TF database such as...

I'll either search against a TF database such as DBD/Pfam or blast the proteins to known TFs.
Forum: Introductions 11-06-2014, 01:34 PM
Replies: 2
Views: 976
Posted By Melissa
Welcome! I think the forum needs more people like...

Welcome! I think the forum needs more people like you who are eager to contribute.

Giant viruses?! Any relation to Jean-Michel Claverie's group?
Forum: Academic/Non-Profit Jobs 07-01-2014, 11:46 AM
Replies: 20
Views: 2,746
Posted By Melissa
You have a point. Occasionally you do get people...

You have a point. Occasionally you do get people who are over-qualified. Recently, my lab received an application for a lab technician position from somebody who has a PhD and is interested to move...
Forum: Academic/Non-Profit Jobs 07-01-2014, 10:47 AM
Replies: 20
Views: 2,746
Posted By Melissa
That's true. But this is the only way to start in...

That's true. But this is the only way to start in academia. Postdoc positions have become so competitive because there are not many jobs around.
Forum: Academic/Non-Profit Jobs 07-01-2014, 10:27 AM
Replies: 20
Views: 2,746
Posted By Melissa
Question Are postdoc job ads these days asking too much from a PhD graduate?

Looking at the bioinformatics postdoc job ads these days, I can't help but wonder if..
a) Some job ads are asking too much from a fresh phD graduate?
a) Or are they trying to recruit people with...
Forum: Epigenetics 04-01-2014, 02:06 PM
Replies: 3
Views: 1,430
Posted By Melissa
I think there must be many similar experiments in...

I think there must be many similar experiments in NCBI SRA unless you're using different cancer cells. If you want to look for histone modifications and methylation patterns, you will need to do...
Forum: Introductions 04-01-2014, 01:45 PM
Replies: 2
Views: 1,978
Posted By Melissa
It depends how clean or how good you want your...

It depends how clean or how good you want your RNA to be. I would recommend the RNA cleanup kit. I usually do ethanol precipitation after DNase digestion because I need to concentrate it anyway.
...
Forum: Bioinformatics 04-01-2014, 01:32 PM
Replies: 2
Views: 1,023
Posted By Melissa
If I were to do this, I would store the consensus...

If I were to do this, I would store the consensus sequences in a pileup format. You might get better ideas after looking at SOAPindel and indelrealigner.
...
Forum: Bioinformatics 04-01-2014, 01:15 PM
Replies: 3
Views: 1,366
Posted By Melissa
Not sure if I understand your question correctly....

Not sure if I understand your question correctly. Here's my opinion on Mummer. It's not updated for a few years. However, I wouldn't call it outdated because many bioinformatians I know including...
Forum: Bioinformatics 02-12-2014, 08:45 AM
Replies: 0
Views: 678
Posted By Melissa
Talking Finding main transcripts from SOAPdenovo-trans results

Hi guys, do you know how I can get the main/best/longest transcripts for each locus in my SOAPdenovo-trans assemblies? I'm not interested in the alternative splicing isoforms. When I used the...
Forum: Illumina/Solexa 12-05-2013, 03:18 PM
Replies: 5
Views: 2,391
Posted By Melissa
The datasets make sense to me because you're not...

The datasets make sense to me because you're not sequencing from all the same individuals. Sequencing bias is also a good explanation. M1 is most similar to G1 because mutation doesn't affect many...
Forum: General 09-08-2013, 09:59 AM
Replies: 18
Views: 8,391
Posted By Melissa
3) This data will not be in my MSc and I won't be...

3) This data will not be in my MSc and I won't be doing much work with it beyond posting here; but I would like to include a short section in my thesis on the data we collect here. Is it possible to...
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