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Search: Posts Made By: Melissa
Forum: General 04-02-2020, 05:43 AM
Replies: 4
Views: 2,128
Posted By Melissa
Hi Rnasoup, Thanks for your reply. What I...

Hi Rnasoup,

Thanks for your reply. What I meant is the data quality in terms of reported phred score vs observed phred score, substitution/indel error rate, problematic region for variant calling...
Forum: General 03-27-2020, 02:18 AM
Replies: 4
Views: 2,128
Posted By Melissa
Hi, Thanks Rnasoup for sharing the link to...

Hi,

Thanks Rnasoup for sharing the link to the sequencing adapter. I tried to find it but nothing showed up in google.

I hope jgroh resolved the adapter issue. It does look quite strange.

By...
Forum: Vendor Forum 03-12-2020, 02:25 AM
Replies: 111
Views: 72,818
Posted By Melissa
Great discussion and thanks for sharing the...

Great discussion and thanks for sharing the plots. In short, Nextseq generates higher error rate in variant calling. This is often overlooked when buying the machine. It poses great challenges for...
Forum: General 12-11-2019, 12:46 AM
Replies: 3
Views: 4,231
Posted By Melissa
Think Uber pool for sequencing. Lol interesting...

Think Uber pool for sequencing. Lol interesting concept!
Forum: The Pipeline 12-11-2019, 12:39 AM
Replies: 1
Views: 8,875
Posted By Melissa
Nice list! Thanks.

Nice list! Thanks.
Forum: General 12-11-2019, 12:32 AM
Replies: 2
Views: 2,489
Posted By Melissa
Pretty interesting! Thanks for the link

Pretty interesting! Thanks for the link
Forum: Bioinformatics 12-10-2019, 04:50 AM
Replies: 1
Views: 784
Posted By Melissa
To find overlapping variants between two files,...

To find overlapping variants between two files, you can use bcftools. If you want to generate a simple venn diagram, you can provide lists to http://bioinformatics.psb.ugent.be/webtools/Venn
Forum: Bioinformatics 12-10-2019, 04:32 AM
Replies: 2
Views: 882
Posted By Melissa
What I will do is to write my own script to 1)...

What I will do is to write my own script to
1) blastn the sequences against itself (hopefully your sequences are long enough to justify using blast)
2) filter the results to remove blastn results...
Forum: General 07-20-2018, 06:52 AM
Replies: 1
Views: 1,793
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: 1,819
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: 1,124
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: 1,392
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: 1,118
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: 2,089
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: 885
Posted By Melissa
Welcome! :)

Welcome! :)
Forum: General 05-08-2015, 12:10 PM
Replies: 5
Views: 2,362
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: 1,478
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: 3,011
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: 2,081
Posted By Melissa
Thanks for the info :)

Thanks for the info :)
Forum: Epigenetics 02-12-2015, 10:03 AM
Replies: 3
Views: 2,081
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: 2,081
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: 1,035
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: 1,239
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: 3,497
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: 3,497
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.
Showing results 1 to 25 of 124

 


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