User: chrys

gravatar for chrys
chrys30
Reputation:
30
Status:
New User
Location:
Germany
Last seen:
1 week, 3 days ago
Joined:
8 months, 1 week ago
Email:
c******************@gmx.de

Posts by chrys

<prev • 16 results • page 1 of 2 • next >
1
vote
1
answer
105
views
1
answer
Meme-Tools: Bit score
... Hi guys, I am currently trying to understand the meme motif finder output and I have a little bit of an issue understanding what the bit score means when looking at the motifs: http://meme-suite.org/doc/examples/meme_example_output_files/meme.html If you look at the sample output, the y-axis on t ...
meme alignment bit score written 10 days ago by chrys30 • updated 10 days ago by Alex Reynolds21k
0
votes
0
answers
259
views
0
answers
Comment: C: Getting multiple *.sra files from NCBI using a list
... Well, it would work but I would still need to acquire the explicit identifier of every experiment since the GEO accession does not work and the compression of *.sra is quite high since I do not need them all at once but iteratively. Also unfortunately, the NIH Roadmap does not let me export the dire ...
written 3 months ago by chrys30
1
vote
0
answers
259
views
0
answers
Getting multiple *.sra files from NCBI using a list
... Hi there folks, I am trying to download SRA files from a dataset I compiled from the NIH Roadmap Data Matrix. The problem is that the dataset spans about 50-60 files. I have little intend of downloading them by hand and I thought a quick wget would help but for some reason each link provided just ho ...
ncbi sra written 3 months ago by chrys30
0
votes
3
answers
344
views
3
answers
Comment: C: Calculating p-Value for an observed/expected Ratio
... Thank you very kindly! You have been a great help. ...
written 5 months ago by chrys30
1
vote
3
answers
344
views
3
answers
Comment: C: Calculating p-Value for an observed/expected Ratio
... Thanks for the help! Will the permutation test p-value also apply if I process the data ? Say I count the reads and do a log transform of the counts. Or better: Does the formula hold true, when I compare the values after I do some sort of processing with it as long as I do the same processing with b ...
written 5 months ago by chrys30
0
votes
3
answers
344
views
3
answers
Comment: C: Calculating p-Value for an observed/expected Ratio
... I thought about using the fishers exact test, but wouldn't I have to calculate the test for every shuffle and then somehow correct the cumulative p-values somehow by say Bonferroni correction ? ...
written 5 months ago by chrys30
11
votes
3
answers
344
views
5 follow
3
answers
Calculating p-Value for an observed/expected Ratio
... Hi, I am performing a shuffle of reads from a ChIP-Seq experiment over some features in the genome and since I do not know the original distributions I am trying to perform an observed to expected calculation to see which features are enriched. Boiled down this means I have counts of reads mappin ...
reads chip-seq written 5 months ago by chrys30 • updated 5 months ago by Ben50
0
votes
1
answer
330
views
1
answers
Comment: C: Remove specific reads from fastq file
... Ah ok thank you very much for that information. I was not aware that old Illumina data contains all N's reads. Maybe just removing x amount of reads at the start of the file will do the trick. ...
written 6 months ago by chrys30
0
votes
1
answer
330
views
1
answers
Comment: C: Remove specific reads from fastq file
... Yes I did. The quality is rather poor but I don't mind the overall quality but for my purpose it is rather important that I don't have to many ambiguous reads in there and there seem to be quite a few with a lot of uncalled bases which I would like to remove. ...
written 6 months ago by chrys30
3
votes
1
answer
330
views
1
answer
Remove specific reads from fastq file
... Hi, I have a fastq file with reads of the following type: > @SRR066153.1 SOLEXA-1GA-2_1:1:1:0:715 length=36 > NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN > +SRR066153.1 SOLEXA-1GA-2_1:1:1:0:715 length=36 > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > @SRR06 ...
reads fastq written 6 months ago by chrys30 • updated 6 months ago by genomax34k

Latest awards to chrys

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1406 users visited in the last hour