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Search: Posts Made By: GenoMax
Forum: Bioinformatics Today, 11:39 AM
Replies: 8
Views: 190
Posted By GenoMax
Run the following to see the difference for...

Run the following to see the difference

for i in `seq 1 120`
do
echo cp $i_*.fastq.gz ~/project1/
done
Forum: Bioinformatics Today, 06:53 AM
Replies: 3
Views: 148
Posted By GenoMax
You will find plenty of real datasets which will...

You will find plenty of real datasets which will (claim to have) low false positive rates (everyone wants to achieve that) but it may be hard to find a real dataset that has high false positive rate...
Forum: Bioinformatics Today, 02:02 AM
Replies: 3
Views: 148
Posted By GenoMax
You could simulate them yourself to have precise...

You could simulate them yourself to have precise control over the "truth".
Forum: Illumina/Solexa Yesterday, 09:22 AM
Replies: 2
Views: 136
Posted By GenoMax
If you use the standard indexes it should be...

If you use the standard indexes it should be fine. Illumina has a white paper somewhere that recommends specific combinations of indexes depending on number of samples you are pooling.
Forum: Illumina/Solexa 10-18-2017, 03:11 AM
Replies: 3
Views: 192
Posted By GenoMax
1000K/mm2 is outside limit per sepc for V2...

1000K/mm2 is outside limit per sepc for V2 chemistry. While it is tempting to push cluster density (trying to get additional data) the fall in data yield/quality is precipitous when you go over a...
Forum: Bioinformatics 10-17-2017, 11:16 AM
Replies: 3
Views: 225
Posted By GenoMax
Have you used Mauve ...

Have you used Mauve (http://darlinglab.org/mauve/mauve.html)to take a look at how your genome looks compared to other known ones?
Forum: Bioinformatics 10-17-2017, 08:40 AM
Replies: 8
Views: 190
Posted By GenoMax
The _ should have been escaped. Corrected code...

The _ should have been escaped. Corrected code above. Replace "echo" instead of "cp" to make sure all looks good first.
Forum: Bioinformatics 10-17-2017, 08:33 AM
Replies: 2
Views: 161
Posted By GenoMax
You could use GitHub (and its markdown code) for...

You could use GitHub (and its markdown code) for creating pages. You could use R notebooks (http://rmarkdown.rstudio.com/r_notebooks.html) or Jupyter notebook (http://jupyter.org/).
Forum: Bioinformatics 10-17-2017, 08:19 AM
Replies: 8
Views: 190
Posted By GenoMax
That should be a $i (not 1). for i in `seq 1...

That should be a $i (not 1).

for i in `seq 1 120`
do
cp $i\_*.fastq.gz ~/project1/
done
Forum: Bioinformatics 10-17-2017, 08:10 AM
Replies: 8
Views: 190
Posted By GenoMax
Where are you copying them from or to? You...

Where are you copying them from or to?

You can generate the numbers you need using a bash for loop like this easily

for i in `seq 1 120`; do echo $i; done
Forum: Bioinformatics 10-16-2017, 08:48 AM
Replies: 3
Views: 255
Posted By GenoMax
I don't know about Europe specifically but the...

I don't know about Europe specifically but the actual university may matter, only if you are planning to stay in academics long-term.

Long as you have demonstrable bioinformatics skills it may...
Forum: Bioinformatics 10-16-2017, 04:39 AM
Replies: 279
Views: 58,577
Posted By GenoMax
Not having reads in sync causes issues with...

Not having reads in sync causes issues with mapping with most aligners (you note that bwa is an exception). I assume only case where R2 would be eliminated (while R1 remains) would be if you were...
Forum: Bioinformatics 10-15-2017, 02:25 PM
Replies: 279
Views: 58,577
Posted By GenoMax
@Dario: Have you tried this with a file that has...

@Dario: Have you tried this with a file that has the (/1 of old Illumina style of 1:N:0 of new read headers)? Interleaved files may need those identifiers to be there. They can be added by...
Forum: Bioinformatics 10-14-2017, 04:54 AM
Replies: 85
Views: 13,556
Posted By GenoMax
Appears that tadpole is not able to take SE,PE...

Appears that tadpole is not able to take SE,PE reads at the same time.
Forum: Bioinformatics 10-13-2017, 10:15 AM
Replies: 85
Views: 13,556
Posted By GenoMax
Axolotl genome paper has used SOAPdenovo2.

Axolotl genome paper has used SOAPdenovo2.
Forum: Bioinformatics 10-13-2017, 09:34 AM
Replies: 85
Views: 13,556
Posted By GenoMax
I am not sure if Tadpole is designed to assemble...

I am not sure if Tadpole is designed to assemble a genome of this size. Curious to see what @Brian has to say.

Have you tried other large genome assemblers? ALLPATHS-LG?
Forum: Core Facilities 10-13-2017, 03:05 AM
Replies: 1
Views: 575
Posted By GenoMax
Call-in details for this call next week: For...

Call-in details for this call next week:

For US, toll free:

1.800.501.8979 (access code 6430305)

For international toll free, Appendix A (page 5/6) of this document contains the toll free,...
Forum: RNA Sequencing 10-12-2017, 04:29 PM
Replies: 2
Views: 264
Posted By GenoMax
This is not an unheard of problem. There have...

This is not an unheard of problem. There have been papers comparing different methods for DE and the results they produce. Here is one of them...
Forum: Bioinformatics 10-12-2017, 07:17 AM
Replies: 53
Views: 11,223
Posted By GenoMax
@Brian is doing something very specific to remove...

@Brian is doing something very specific to remove human contamination in JGI's non-human samples.

Re-reading your original question it would be good to know if your contaminants are "close"...
Forum: Bioinformatics 10-12-2017, 04:40 AM
Replies: 53
Views: 11,223
Posted By GenoMax
While Brian will have a more detailed insight it...

While Brian will have a more detailed insight it should be ok to use the unmasked genome with BBSplit. Any mapping issues you may have with short reads should be more or less same with genome or just...
Forum: Bioinformatics 10-11-2017, 03:57 PM
Replies: 1
Views: 251
Posted By GenoMax
Multiple options to do this in this Biostars...

Multiple options to do this in this Biostars thread (https://www.biostars.org/p/49820/).
Forum: Bioinformatics 10-11-2017, 03:52 PM
Replies: 112
Views: 36,791
Posted By GenoMax
That is overly strict. What type of dataset is...

That is overly strict. What type of dataset is this and do you have a reference genome available?
Forum: Events / Conferences 10-11-2017, 07:21 AM
Replies: 2
Views: 159
Posted By GenoMax
Are the course materials available outside of...

Are the course materials available outside of actually taking this class?
Forum: Bioinformatics 10-09-2017, 03:36 PM
Replies: 573
Views: 99,762
Posted By GenoMax
@Brian: K-mer module in FastQC only tracks 2% of...

@Brian: K-mer module in FastQC only tracks 2% of the data (1 in 50 sequences)
Forum: Bioinformatics 10-09-2017, 11:29 AM
Replies: 3
Views: 226
Posted By GenoMax
Merged fastq files should be identical...

Merged fastq files should be identical representations of individual pieces unless whatever fusion program you used had trouble completely reading the merged files. Did you check to make sure the...
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