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Search: Posts Made By: wdecoster
Forum: Bioinformatics 10-18-2017, 03:01 AM
Replies: 2
Views: 431
Posted By wdecoster
I've done something similar, using a few genes...

I've done something similar, using a few genes which are gender specific, rather than only Y chromosome genes. Note that you should think about the pseudoautosomal regions.

I right now don't have...
Forum: Bioinformatics 08-13-2017, 04:16 AM
Replies: 1
Views: 538
Posted By wdecoster
Have a look at this paper...

Have a look at this paper (https://www.ncbi.nlm.nih.gov/pubmed/26492578) in which this cg homwes tool (http://genomecomb.sourceforge.net/docs/cg_homwes.html) is described.

Disclaimer: tool and...
Forum: Bioinformatics 07-13-2017, 03:34 AM
Replies: 5
Views: 617
Posted By wdecoster
Everything would be fixed if you can get the bam...

Everything would be fixed if you can get the bam files, then you can do your own analysis. Getting counts (in R) is easy, doing differential expression analysis isn't too hard.
Forum: Bioinformatics 07-12-2017, 12:14 AM
Replies: 1
Views: 365
Posted By wdecoster
featureCounts and htseq-count are the most...

featureCounts and htseq-count are the most commonly used tools, but you could also use Salmon (with or without alignment) or kallisto (without alignment).
Forum: Bioinformatics 06-06-2017, 11:43 PM
Replies: 6
Views: 516
Posted By wdecoster
Which python version are you using?

Which python version are you using?
Forum: Bioinformatics 06-02-2017, 02:20 AM
Replies: 3
Views: 418
Posted By wdecoster
That's probably it. Also, it's very helpful to...

That's probably it. Also, it's very helpful to show the error message you get.
Forum: Bioinformatics 04-24-2017, 11:50 PM
Replies: 4
Views: 669
Posted By wdecoster
In short, because those variants have (due to...

In short, because those variants have (due to technical difficulties) a high chance of being false-positive.
Forum: Oxford Nanopore 04-04-2017, 04:28 AM
Replies: 8
Views: 1,929
Posted By wdecoster
No, but I should note that I still have to update...

No, but I should note that I still have to update our installation to the latest version.
Forum: Bioinformatics 04-03-2017, 09:57 PM
Replies: 3
Views: 631
Posted By wdecoster
Always the first thing to check is if your fasta...

Always the first thing to check is if your fasta and gtf use the same chromosome notation.
Forum: Oxford Nanopore 04-02-2017, 09:17 AM
Replies: 8
Views: 1,929
Posted By wdecoster
I installed it because the Windows version was...

I installed it because the Windows version was being annoying. The problem was solved on Ubuntu16.04, but we haven't started a run yet so can't I comment on that.
Forum: Bioinformatics 03-31-2017, 01:37 PM
Replies: 10
Views: 1,571
Posted By wdecoster
Classic mistake, but you'll make this one only...

Classic mistake, but you'll make this one only once ;)
Forum: Bioinformatics 03-31-2017, 03:03 AM
Replies: 1
Views: 544
Posted By wdecoster
What is that function supposed to do?

What is that function supposed to do?
Forum: Bioinformatics 03-27-2017, 02:46 PM
Replies: 13
Views: 997
Posted By wdecoster
You should use the whole dataset and later on...

You should use the whole dataset and later on check if the genes up and down regulated correspond to a certain function.
Forum: Bioinformatics 02-28-2017, 09:37 PM
Replies: 5
Views: 700
Posted By wdecoster
For question 1, the increase in %A is not too...

For question 1, the increase in %A is not too bad. I think it can be explained that for some reads you start running in the polyA tail, which you might want to trim off.
Forum: RNA Sequencing 02-23-2017, 09:34 AM
Replies: 5
Views: 1,035
Posted By wdecoster
But that is a violation of independent filtering...

But that is a violation of independent filtering principle, you cannot filter for something you are testing for. Obviously it is great for your p-values, but also completely invalid and should be...
Forum: Bioinformatics 02-15-2017, 05:54 AM
Replies: 2
Views: 640
Posted By wdecoster
I would try something like: for file in...

I would try something like:
for file in *_pandaseq.fasta
do
newname=$(echo $file | sed s/_pandaseq.fasta//)
awk '/^>/{print $newname ++i; next}{print}' $file > ${newname}_pandaseq_new.fasta
done
Forum: Bioinformatics 02-14-2017, 07:50 AM
Replies: 7
Views: 1,883
Posted By wdecoster
I would assume the following should work: (but...

I would assume the following should work:
(but obviously untested)

for f in $(ls *.fastq.gz | sed 's/?_001.fastq.gz//' | sort -u)
do
java -jar ~/Trimmomatic-0.36/trimmomatic-0.36.jar PE...
Forum: Bioinformatics 02-13-2017, 11:36 PM
Replies: 2
Views: 530
Posted By wdecoster
The population you are studying will hugely...

The population you are studying will hugely influence this. If you are working on commonly sequenced individuals such as European Americans the frequency of "known" variants will be much compared to...
Forum: Bioinformatics 02-13-2017, 09:59 AM
Replies: 4
Views: 554
Posted By wdecoster
I would assume a quick way would be if you couple...

I would assume a quick way would be if you couple bedtools getfasta with a tool such as VEP or snpeff...
Forum: Oxford Nanopore 02-11-2017, 07:59 AM
Replies: 9
Views: 2,264
Posted By wdecoster
The error rate is also species-dependent. If I'm...

The error rate is also species-dependent. If I'm not mistaken the basecaller is mainly trained on the e.colli and lambda genome. Improvements to base calling for human genomes will happen if training...
Forum: Bioinformatics 02-09-2017, 10:00 PM
Replies: 3
Views: 485
Posted By wdecoster
To me, your question is very unclear, either this...

To me, your question is very unclear, either this "Fasta reference tool maker software" is something I'm completely unaware of or it's not well specified what you are looking for. Can you add some...
Forum: Bioinformatics 01-31-2017, 05:56 AM
Replies: 1
Views: 602
Posted By wdecoster
Most commonly log scaling is used. Recommended is...

Most commonly log scaling is used. Recommended is probably to use DESeq2 or similar to extract log normalized counts with a more sophisticated model than RPKM.
Forum: Bioinformatics 01-26-2017, 12:04 AM
Replies: 4
Views: 843
Posted By wdecoster
That's not how you should write fasta output...

That's not how you should write fasta output...
Forum: Bioinformatics 01-25-2017, 07:15 AM
Replies: 6
Views: 1,144
Posted By wdecoster
But reading is hard and takes time, therefore...

But reading is hard and takes time, therefore it's easier to just ask people who volunteer online to help and waste their time instead.
Forum: Bioinformatics 01-25-2017, 12:26 AM
Replies: 4
Views: 843
Posted By wdecoster
Now you are writing here a literal "fasta" string...

Now you are writing here a literal "fasta" string on the end of every line. I doubt whether that's what you have in mind. What about this?


from Bio import SeqIO

out = open("try_out.fasta",...
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