Forum: Sample Prep / Library Generation
09-13-2020, 11:20 PM
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Replies: 1
Views: 3,326
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Forum: Sample Prep / Library Generation
01-19-2019, 11:18 PM
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Replies: 0
Views: 1,030
Crispr library which gene?
Hi,
we're planning to do several Crispr runs to answer several question relating to translational machinery.
I was wondering whether there are prepared libraried for such experiments, or if one...
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Forum: Bioinformatics
11-13-2018, 11:47 PM
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Replies: 4
Views: 2,313
I just wanted to add that this case is even...
I just wanted to add that this case is even stranger, as i have this sample, where the GC content is classified as good, even though it is completely shifted to the left.
Q: How does fastqc...
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Forum: Bioinformatics
11-13-2018, 11:39 PM
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Replies: 4
Views: 2,313
fastqc shows strange GC content
Hi,
we have a 36-samples ChIP-Seq experiment with a very strange GC-content behavior (s. images)
The samples are from yeast. This strange behavior comes in the IP samples, some of them shows (the...
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Forum: Bioinformatics
02-10-2018, 08:48 AM
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Replies: 0
Views: 2,078
long noncoding RNA DE analysis
Hi everybody,
I am looking for a method/tool/workflow to analyse the differential expression of long ncRNA in C. elegans.
After searching the web for quite some time, I can't find a complete...
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Forum: Bioinformatics
11-22-2017, 05:25 AM
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Replies: 0
Views: 1,259
Pol III chip-seq experimental design
hi all,
we are planning on doing a ChIP-Seq experiment trying to identify PolIII binding sites in yeast and mouse.
As I am not really sure of the binding affinity of PolII I would like to ask for...
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Forum: Bioinformatics
11-07-2017, 02:15 AM
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Replies: 1
Views: 1,683
library depths for sequencing
Hi everybody,
I was approached by a biologist in our lab and was ask a specific question. As I was not really sure, I would like to share it with the community and hope to get some answers from...
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Forum: Bioinformatics
06-28-2016, 05:11 AM
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Replies: 1
Views: 1,854
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Forum: Bioinformatics
06-28-2016, 01:38 AM
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Replies: 1
Views: 1,854
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Forum: Bioinformatics
05-24-2016, 03:27 AM
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Replies: 0
Views: 1,683
extending reads in ChIP-Seq analysis
Hi,
we're working on a ChIP-Seq data set. I have read in some tutorials and workflows that after mapping the reads, they should be extended to the estimated fragment size.
Am I correct in the...
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Forum: Events / Conferences
05-02-2016, 12:32 AM
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Replies: 2
Views: 2,562
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Forum: Bioinformatics
04-12-2016, 10:52 AM
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Replies: 1
Views: 3,789
hisat2 output more reads than are in the file
Hi all,
I am in the middle of testing the hisat2 mapper and encountered a discrepancy between the output hisat2 gives me at the end of the mapping step and the number of reads samtools flagstat...
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Forum: Bioinformatics
04-06-2016, 03:16 AM
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Replies: 0
Views: 2,779
running DEXSeq with hisat2 created bam files
Hi,
I am trying to run DEXSeq with bame files made by the hisat2 mapper. I have created the gff file according to the manual. I have seen that the chromosome names are different from the bam...
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Forum: Bioinformatics
04-04-2016, 01:39 AM
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Replies: 0
Views: 1,853
interpreting preseq results
Hi,
I am running the preseq c_curve and lc_extrap on a few fastq files using the option -V.
(Q: does it make sense at all to run preseq on the fastq files, or will it be more accurate, when...
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Forum: Bioinformatics
03-10-2016, 11:34 PM
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Replies: 2
Views: 6,965
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Forum: Bioinformatics
03-10-2016, 11:27 PM
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Replies: 2
Views: 6,965
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Forum: Bioinformatics
11-27-2015, 04:31 AM
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Replies: 2
Views: 3,509
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Forum: Bioinformatics
11-26-2015, 02:22 AM
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Replies: 2
Views: 3,509
fastqc Exception (error)
Hi,
I am running the fastqc (v0.11.4) on Ubuntu 14.04.3 LTS.
I have four fastq files (two pairs of paired-end reads samples). They are AFAIK from old solexa machines in sanger format
somehow...
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Forum: Bioinformatics
11-22-2015, 10:32 PM
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Replies: 22
Views: 8,871
Hi Devon,
you mentioned, being picky can be...
Hi Devon,
you mentioned, being picky can be a virtue, so I'm being picky again.
I was wondering about my first question for the comparison between the knock-out and the stimulation. I wanted...
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Forum: Bioinformatics
11-18-2015, 01:59 AM
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Replies: 7
Views: 3,085
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Forum: Bioinformatics
11-18-2015, 01:15 AM
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Replies: 7
Views: 3,085
DEXSeq error with paired-end data
Hi,
I'm trying to run rhe python script for counting the reads for a dexseq analysis.
But I keep getting a strange error I can't understand
python...
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Forum: Bioinformatics
11-18-2015, 12:25 AM
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Replies: 22
Views: 8,871
Yes, it helps a lot. I think I start :(...
Yes, it helps a lot. I think I start :( understanding it.
I have another question about the colData. Does the order of the samples here must be the same as in the count table.
I am asking because...
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Forum: Bioinformatics
11-17-2015, 07:47 AM
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Replies: 22
Views: 8,871
Sorry to be so picky, but I still have some...
Sorry to be so picky, but I still have some difficulties understanding it, even if it might not seems this way.
What would be the difference between the two models:
~condition + stimulation
and...
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Forum: Bioinformatics
11-17-2015, 05:08 AM
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Replies: 22
Views: 8,871
thanks again,
if I take one of the...
thanks again,
if I take one of the names from my resultNames() vector:
> resultsNames(dds)
[1] "Intercept" "condition_wildtype_vs_trippleKO"
[3]...
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Forum: Bioinformatics
11-17-2015, 04:39 AM
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Replies: 22
Views: 8,871
Hi all,
thanks Devon for all the help. It...
Hi all,
thanks Devon for all the help. It seems to works quite good.
Just to make sure I have understood the way to create the multi-factor designs I was asked by a college of mine about a...
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