SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 35
Search took 0.00 seconds.
Search: Posts Made By: jiaco
Forum: Bioinformatics 06-18-2019, 08:18 AM
Replies: 6
Views: 1,522
Posted By jiaco
It is just something you need to know. I switched...

It is just something you need to know. I switched my source of fasta at the same time as I started trying bbmap. The aligner seemed much better than the one I was using before and then I ran it on a...
Forum: Bioinformatics 06-18-2019, 04:31 AM
Replies: 6
Views: 1,522
Posted By jiaco
Ran into the same problem recently, with over 500...

Ran into the same problem recently, with over 500 bams to further process, I went the reheader route, but it would seem based on the comment "BBMap is one of few aligners that passes along the entire...
Forum: Bioinformatics 01-04-2017, 06:17 AM
Replies: 19
Views: 4,406
Posted By jiaco
Curious if anyone on here agrees with me on this,...

Curious if anyone on here agrees with me on this, but IMO what is needed is something that works both with and without GUI. If you want bioinformaticans to care, you cannot force them to touch the...
Forum: Academic/Non-Profit Jobs 01-09-2015, 04:41 AM
Replies: 0
Views: 1,090
Posted By jiaco
Bioinformatician (Metagenomics) position in Toulouse, France

A 3 year postdoctoral engineer position will be open in spring 2015 in the Functional Genomics of Metabolic Diseases Unit of the I2MC in Toulouse, France. The position is aimed at a computational...
Forum: Academic/Non-Profit Jobs 01-07-2015, 02:29 AM
Replies: 0
Views: 1,378
Posted By jiaco
Biostatistician/Bioinformatician position in Toulouse, France

A 1 year (2 years with extension) postdoctoral position is open in the Obesity Research Unit of the I2MC in Toulouse, France. The position is aimed at a computational biologist, with an emphasis on...
Forum: UK - Cambridge 05-21-2014, 12:18 AM
Replies: 5
Views: 9,388
Posted By jiaco
Thanks for replying. Yes, we are studying...

Thanks for replying.

Yes, we are studying multiple modifications (multiple antibodies) and have 2 conditions (treatments) so I need a way to normalize data from the same antibody in different...
Forum: UK - Cambridge 05-20-2014, 11:56 PM
Replies: 5
Views: 9,388
Posted By jiaco
I came here this morning to start a very similar...

I came here this morning to start a very similar thread. So instead will bump this one, although I admit, I am not exactly sure what this subsection of the forum is for. If I need to start a new...
Forum: Academic/Non-Profit Jobs 01-11-2013, 12:38 AM
Replies: 0
Views: 1,567
Posted By jiaco
2 year Bioinformatics position in Toulouse, France

Two year Bioinformatics position at the Laboratory of Molecular and Cellular Biology of Cell Proliferation Control, CNRS UMR5088 in Toulouse, France

A two year contract for a Bioinformatics...
Forum: Bioinformatics 12-22-2012, 01:20 AM
Replies: 5
Views: 2,517
Posted By jiaco
You could expand the expression to match ...

You could expand the expression to match

/^[ACGT].*+$/

to avoid quality lines, but I have no idea where you got the file, let alone how it got corrupted.

EDIT: saw your new example just now,...
Forum: Bioinformatics 12-22-2012, 12:04 AM
Replies: 5
Views: 2,517
Posted By jiaco
If this problem is consistent throughout the file...

If this problem is consistent throughout the file


sed "s/+$/\\`echo -e '\n\r'`+/g" bad.fastq > good.fastq

should do the trick.

EDIT: never remember adding a newline with sed to be...
Forum: Bioinformatics 12-18-2012, 12:32 AM
Replies: 5
Views: 1,887
Posted By jiaco
Yeah, something fun to do first thing this...

Yeah, something fun to do first thing this morning. Despite the functional hack by R Finney, here is another that gets you the image in pdf format.


Put the first code block in wgetUcscPdfs.sh...
Forum: Bioinformatics 12-14-2012, 02:46 AM
Replies: 3
Views: 1,285
Posted By jiaco
wget -r -nd -A *.ncrna.fa.gz...

wget -r -nd -A *.ncrna.fa.gz ftp://ftp.ensembl.org/pub/release-69/fasta


this seems to work.
Forum: Bioinformatics 12-01-2012, 02:05 PM
Replies: 3
Views: 3,606
Posted By jiaco
Are you sure the supervisor did not mean 10...

Are you sure the supervisor did not mean 10 promoters for 1 gene but from 10 different organisms? Unless the gene of interest has 10 different TSSs, I do not understand the question unless it means...
Forum: Bioinformatics 11-30-2012, 06:02 AM
Replies: 2
Views: 1,756
Posted By jiaco
biomaRt (R/bioconductor):...

biomaRt (R/bioconductor): http://www.bioconductor.org/packages/2.11/bioc/html/biomaRt.html


library( biomaRt )

uniprot = useMart( "unimart" );
uniprot = useDataset( "uniprot", uniprot );

#...
Forum: Bioinformatics 11-27-2012, 06:34 AM
Replies: 4
Views: 1,971
Posted By jiaco
make a new user without any spaces and build it...

make a new user without any spaces and build it under that user.
otherwise you will have to edit the makefiles and put quotes around the path...
Forum: Bioinformatics 11-27-2012, 05:47 AM
Replies: 13
Views: 2,532
Posted By jiaco
I would love to see vi extended to handle...

I would love to see vi extended to handle alignments.

Specifically, searches for sequences and patterns that ignore '-'/gaps and the ability to also find those patterns in reverse complement space.
Forum: Bioinformatics 11-27-2012, 05:44 AM
Replies: 4
Views: 1,971
Posted By jiaco
This line right here: "cd: /Users/Jo: No such...

This line right here: "cd: /Users/Jo: No such file or directory"
is giving you a hint? Does the path exist? Maybe your username has a space in it?
Forum: 454 Pyrosequencing 02-01-2012, 11:21 AM
Replies: 7
Views: 5,102
Posted By jiaco
Sadly, you miss the sff file. You need to read...

Sadly, you miss the sff file. You need to read this:

http://www.mothur.org/wiki/Schloss_SOP

Mothur and Qiime can both process this type of data, but I find the Mothur wiki a bit more...
Forum: Bioinformatics 02-01-2012, 11:19 AM
Replies: 5
Views: 2,203
Posted By jiaco
Did you try mingw-w64? ...

Did you try mingw-w64?
http://mingw-w64.sourceforge.net/
Forum: 454 Pyrosequencing 01-26-2012, 02:39 PM
Replies: 12
Views: 6,877
Posted By jiaco
@HMorrison - we actually barcoded both ends. I...

@HMorrison - we actually barcoded both ends. I have been working the last week or so getting programs in place to basically prove the data we have is crap and that we deserve a refund from the...
Forum: Bioinformatics 01-18-2012, 11:29 AM
Replies: 1
Views: 2,023
Posted By jiaco
If you have log2 data and geneA is 8.0 in cancer...

If you have log2 data and geneA is 8.0 in cancer and 6.0 in control, you have a 2.0 log2ratio (cancer-control). Which is 2^2 = 4 in fold change. But the ratio in (control-cancer) is -2 and 2^-2 is...
Forum: General 01-13-2012, 10:01 PM
Replies: 9
Views: 3,084
Posted By jiaco
Whatever route you go in terms of analysis and...

Whatever route you go in terms of analysis and programming, make sure to start with a program that can cut your input size down considerably. You want to be able to play with the steps in an analysis...
Forum: 454 Pyrosequencing 01-11-2012, 08:22 AM
Replies: 12
Views: 6,877
Posted By jiaco
Just got off the phone with a company that...

Just got off the phone with a company that provides 454 and have learned a bunch of stuff. Would love to get feedback if anyone has anything to add.

Basically, they agreed that double stranded...
Forum: 454 Pyrosequencing 01-11-2012, 12:27 AM
Replies: 12
Views: 6,877
Posted By jiaco
Thanks to all that have replied so far. It looks...

Thanks to all that have replied so far. It looks like I am going to have to learn a lot more about the technology aspects of this before I can really understand.

But 2 simple questions:

1) Is...
Forum: 454 Pyrosequencing 01-10-2012, 12:42 AM
Replies: 12
Views: 6,877
Posted By jiaco
16S metagenome sequencing directions(F/R)

Dear SEQanswers

I have a very general question and would love to have input from at least a handful of different people with experience in this field.

We are doing 16S profiling of bacteria...
Showing results 1 to 25 of 35

 


All times are GMT -8. The time now is 11:45 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO