SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 121
Search took 0.01 seconds.
Search: Posts Made By: Michael.Ante
Forum: Bioinformatics 10-24-2017, 11:41 PM
Replies: 2
Views: 1,313
Posted By Michael.Ante
Hi DMNO, did you take the transcripts'...

Hi DMNO,

did you take the transcripts' strand-orientation into account? Try using RSeQC's infer-experiment tool (http://rseqc.sourceforge.net/#infer-experiment-py). It gives you a good way to...
Forum: Bioinformatics 02-20-2017, 11:36 PM
Replies: 1
Views: 1,536
Posted By Michael.Ante
I don't know if it's a good idea to do it this...

I don't know if it's a good idea to do it this way, since you'll get a higher amount of overlapping features. I hope you have a stranded library.

Nevertheless, in order to get what you described...
Forum: RNA Sequencing 02-16-2017, 12:03 AM
Replies: 4
Views: 1,457
Posted By Michael.Ante
Hi Danielle, I hope it's not to late for a...

Hi Danielle,

I hope it's not to late for a suggestion. The Genecode and ENSEMBL annotations include in their gtf files per gene a field called "gene_biotype".
If you use htseq-count (for...
Forum: Bioinformatics 01-24-2017, 12:00 AM
Replies: 2
Views: 1,517
Posted By Michael.Ante
Hi bbm, I think the problem is not the name...

Hi bbm,

I think the problem is not the name field, but the missing information on exon-intron structure (since the function "convertBed2Introns" called the error).
Parsing a GFF3 file into...
Forum: Bioinformatics 01-11-2017, 12:50 AM
Replies: 1
Views: 1,130
Posted By Michael.Ante
Hi Marcos, It seems that your plant is a...

Hi Marcos,

It seems that your plant is a model species and well annotated. You could download the gene annotation and extract the 5' and 3' UTR from the gff3 file.
In order to incorporate the...
Forum: Bioinformatics 12-20-2016, 01:07 PM
Replies: 9
Views: 3,119
Posted By Michael.Ante
It should be something like awk...

It should be something like
awk 'NR%4==2{print}' in.fastq | wc
With the awk command, you print the nucleotides, with wc you count the output's characters.
Forum: Bioinformatics 12-19-2016, 07:45 AM
Replies: 16
Views: 4,476
Posted By Michael.Ante
Did you see this pattern also with the...

Did you see this pattern also with the "--nogroup" option?
The bases are binned without that option; which let the distribution may look smoother than it is. The last base, shown in your figure, is...
Forum: RNA Sequencing 12-15-2016, 03:57 AM
Replies: 18
Views: 3,297
Posted By Michael.Ante
Hi chiayi, in your BBmap index, the naming...

Hi chiayi,

in your BBmap index, the naming of the chromosome is "Chr2 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02", whilst in the Hisat alignment it's just "Chr2". Either...
Forum: Bioinformatics 11-29-2016, 02:21 AM
Replies: 5
Views: 4,549
Posted By Michael.Ante
Try as a first solution: countdata <-...

Try as a first solution:
countdata <- as.matrix(read_excel("DEseqcounts.xlsx"),header=TRUE, row.names=1)

And check then
summary(is.numeric(countdata[,1]))

Maybe there are some empty lines...
Forum: Bioinformatics 11-28-2016, 10:51 PM
Replies: 5
Views: 4,549
Posted By Michael.Ante
I'm not so familiar with the stringtie pipeline,...

I'm not so familiar with the stringtie pipeline, but I recommend avoiding Excel for most NGS related analyses (see Zeeberg et al. 2004: Mistaken Identifiers: Gene name errors can be introduced...
Forum: RNA Sequencing 10-06-2016, 12:24 AM
Replies: 5
Views: 1,464
Posted By Michael.Ante
Hi, Before alignment I'd perform QC with...

Hi,

Before alignment I'd perform QC with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)and FastQC screen (http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/)...
Forum: Bioinformatics 09-22-2016, 01:13 AM
Replies: 5
Views: 2,342
Posted By Michael.Ante
Maybe you have also the wrong file: vs.

Maybe you have also the wrong file:


vs.
Forum: Bioinformatics 09-22-2016, 12:37 AM
Replies: 5
Views: 2,342
Posted By Michael.Ante
Hi, did you got any error messages, while...

Hi,

did you got any error messages, while doing:

?
You forgot to include the header which should lead to a non-functional bam file.
Please try samtools view -bSh output_E1.sam >...
Forum: Bioinformatics 09-20-2016, 02:45 AM
Replies: 4
Views: 1,315
Posted By Michael.Ante
The bam_stat.py was a suggestion since it also...

The bam_stat.py was a suggestion since it also works for DNA-seq alignments (you'll hopefully don't see spliced reads).
You can also have a look at the QC-metrics from Picard tools, or have a look...
Forum: Bioinformatics 09-20-2016, 12:19 AM
Replies: 4
Views: 1,315
Posted By Michael.Ante
Hi Rangika, 2nd first: You need to be...

Hi Rangika,

2nd first:
You need to be aware of the fact that samtools flagstat produces statistics on alignments. Meaning, a read can align multiple time and will occur multiple times in the...
Forum: Bioinformatics 09-07-2016, 12:00 AM
Replies: 3
Views: 1,436
Posted By Michael.Ante
I'm sure bbmap...

I'm sure bbmap (http://seqanswers.com/forums/showthread.php?t=41057) can do that.
STAR works very well with Illumina reads and the guys from Pacific Bioscience did some parameter optimisation to...
Forum: Bioinformatics 09-06-2016, 06:48 AM
Replies: 15
Views: 2,734
Posted By Michael.Ante
Not in the first 6 month; that the usual...

Not in the first 6 month; that the usual probation period. In this period you can be fired without reasons, but you can also just leave.
After this period it is clearly more difficult to fire...
Forum: RNA Sequencing 08-25-2016, 10:41 PM
Replies: 6
Views: 1,583
Posted By Michael.Ante
Hi Sebastian, the latest versions of STAR...

Hi Sebastian,
the latest versions of STAR report the NH field. In older versions you should be able to report the number of hits with an according parameters setting.
Forum: RNA Sequencing 08-23-2016, 12:14 AM
Replies: 6
Views: 1,583
Posted By Michael.Ante
Hi Sebastian, You should have a look at the...

Hi Sebastian,

You should have a look at the rRNA content. Download just the sheep's rRNA sequences from NCBI as fasta, create a bowtie2 index, and map the reads with bowtie2 against them. The...
Forum: RNA Sequencing 05-24-2016, 10:47 PM
Replies: 6
Views: 2,983
Posted By Michael.Ante
Hi Ivygreen, did you receive the same map...

Hi Ivygreen,

did you receive the same map mass as with cuffdiff? If not, you can use e.g. R to analyse the genes.fpkm_tracking and isoforms.fpkm_tracking files. For instance, you can make a...
Forum: RNA Sequencing 05-24-2016, 07:32 AM
Replies: 1
Views: 1,702
Posted By Michael.Ante
Hi meabh, First, the main difference is that...

Hi meabh,

First, the main difference is that TopHat2 is designed to detect and report spliced reads. Whenever there is s a read spanning two exons, you'll see that with TopHat2 alignment. The...
Forum: Bioinformatics 05-18-2016, 03:41 AM
Replies: 2
Views: 1,378
Posted By Michael.Ante
Hi Heso, You can use RSeQC's bam2fq.py...

Hi Heso,

You can use RSeQC's bam2fq.py (http://rseqc.sourceforge.net/#bam2fq-py) to make a fastq file out of your "out_no_feature.sam".
In order to get the header into your files, use: samtools...
Forum: Bioinformatics 05-13-2016, 04:22 AM
Replies: 4
Views: 1,372
Posted By Michael.Ante
Hi, A) and B) are different releases of the...

Hi,

A) and B) are different releases of the Human gene assembly. So don't mix them.
If you want to have a bowtie index and its corresponding transcriptome index, download the Fasta files and the...
Forum: Bioinformatics 05-13-2016, 04:08 AM
Replies: 4
Views: 1,476
Posted By Michael.Ante
Hi, it looks, as you have a random-primer in...

Hi,
it looks, as you have a random-primer in the first 8-9 bases. It might be useful to either trim this sequence or increase allowed mismatches in your alignment.

Regarding the over-represented...
Forum: General 05-11-2016, 12:01 AM
Replies: 3
Views: 1,542
Posted By Michael.Ante
For adding error bars (there is a bit more coding...

For adding error bars (there is a bit more coding involved) you can use the arrow function in R.
There are a couple of blogs how to do that. For example, have a look at Monkey's Uncle...
Showing results 1 to 25 of 121

 


All times are GMT -8. The time now is 12:01 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO