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Forum: Bioinformatics 02-24-2016, 11:55 PM
Replies: 10
Views: 3,809
Posted By Alex852013
That's what i did. I used the same amount of...

That's what i did. I used the same amount of cells, added the ERCCs (i took 1 Ál diluted this one 1:100 and added 10 Ál to each tube (better than 1 Ál from a 1:10 dilution to avoid a strong pipetting...
Forum: Bioinformatics 02-24-2016, 08:29 AM
Replies: 10
Views: 3,809
Posted By Alex852013
@ SylvainL: The paper "Revisiting Global...

@ SylvainL:

The paper "Revisiting Global Gene Expression Analysis" was thought to give people an idea of the problem i'm facing. I don't think it makes sense to discuss the quality here.
To give...
Forum: Bioinformatics 02-24-2016, 04:12 AM
Replies: 10
Views: 3,809
Posted By Alex852013
Could you please write what part you mean? If you...

Could you please write what part you mean? If you start with the first few words of the text it will be easier to find. Thanks.

I used the ERCCs, because i think that my factor might upregulate a...
Forum: Bioinformatics 02-24-2016, 03:24 AM
Replies: 10
Views: 3,809
Posted By Alex852013
Up to date ERCC spike ins RNA seq analysis

Hello everybody,

I'm expecting to get my ERCC spiked RNA seq sequencing files soon.
Therefore i would like to find out what's the best way to analyze them.
There are several post where people...
Forum: Bioinformatics 01-07-2016, 11:53 PM
Replies: 8
Views: 2,007
Posted By Alex852013
Yes, it meant 23 % more, which makes 96 % in...

Yes, it meant 23 % more, which makes 96 % in total. Perfect!
Nevertheless, thanks for caring!
Forum: Bioinformatics 01-07-2016, 08:51 AM
Replies: 6
Views: 1,349
Posted By Alex852013
Thanks a lot! Sorry, i didn't see that you...

Thanks a lot!
Sorry, i didn't see that you changed your post.
This solution is not what i thought of, but it's easy and solves the problem :)
Thank you.
Forum: Bioinformatics 01-07-2016, 08:26 AM
Replies: 6
Views: 1,349
Posted By Alex852013
So this will start with this file: ...

So this will start with this file:
10pct-0_S3_R1_001.fastq
use it as placeholder and also use this file for the second placeholder:
->10pct-0_S3_R2_001.fastq<-
Nevertheless, as soon as the first...
Forum: Bioinformatics 01-07-2016, 07:41 AM
Replies: 6
Views: 1,349
Posted By Alex852013
Thanks a lot for the quick reply! Now i run...

Thanks a lot for the quick reply!
Now i run into the trouble, that i only need to choose every 2nd file.
I wanted to start by listing all files ending with fastq and putting them into a variable,...
Forum: Bioinformatics 01-07-2016, 05:20 AM
Replies: 6
Views: 1,349
Posted By Alex852013
Automated script for paired end sequencing

Hello everybody,

I have a folder with paired end sequencing data (divided by the asterisk to make group clearly visible here). I would like to run an automated script, which analyses couple by...
Forum: Bioinformatics 01-07-2016, 04:40 AM
Replies: 8
Views: 2,007
Posted By Alex852013
Thanks for the hint. My adviser told me it is...

Thanks for the hint. My adviser told me it is sufficient to use Bowtie 1.
I tested Bowtie 2 now and i got 10 % more alligned reads. For another sample even 23 %, which is really a lot!
Thanks...
Forum: Bioinformatics 01-05-2016, 06:05 AM
Replies: 8
Views: 2,007
Posted By Alex852013
I got it on my own, after a short break. I forgot...

I got it on my own, after a short break. I forgot to sort the bam files...
Forum: Bioinformatics 01-05-2016, 05:41 AM
Replies: 8
Views: 2,007
Posted By Alex852013
Problem somewhere during paired-end seq analysis -> no reads mapped

Hello everybody,

this is my fist time to try to handle to analyze paired-end sequencing files.
Finally BamCoverage complained there are no mapped reads in my Bam file. Also IGV doesn't show any...
Forum: Bioinformatics 12-04-2015, 05:50 AM
Replies: 136
Views: 40,561
Posted By Alex852013
Thanks a lot

Thanks a lot, i guess i can go on on my own now!
Forum: Bioinformatics 12-03-2015, 07:34 AM
Replies: 136
Views: 40,561
Posted By Alex852013
Understand the quality trimming

Hello everybody,

it is the first time i try to use trim_galore for quality trimming of paired end reads.
I checked for the sequencing settings with testformat.sh from BBMap which gives me:...
Forum: Introductions 12-02-2015, 08:05 AM
Replies: 3
Views: 2,063
Posted By Alex852013
Thanks

Thanks a lot, if now the following mapping step also works, this will be the solution :)
Forum: Introductions 12-01-2015, 09:18 AM
Replies: 3
Views: 2,063
Posted By Alex852013
Struggling with quality trimming

Hello everybody,

this is my first try to trim Illumina (paired-end) reads on the unix command line.
If i get it correctly, de-multiplexing was already done by the sequencing service.
I guess...
Forum: Bioinformatics 07-02-2015, 05:36 AM
Replies: 1
Views: 1,146
Posted By Alex852013
More than 300.000 peaks for a viral transcription factor - what could this mean?

I was told it is better to keep it in one forum, sorry I'm new to forums:

https://www.biostars.org/p/149172/

Hello everybody,

I'm a PhD student and i'm working with a viral transcription...
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