User: johannes.helmuth

Reputation:
110
Status:
New User
Location:
Berlin, Germany
Website:
http://www.gplus.to/he...
Last seen:
6 years, 2 months ago
Joined:
6 years, 9 months ago
Email:
j***************@gmail.com

Posts by johannes.helmuth

<prev • 6 results • page 1 of 1 • next >
0
votes
2
answers
4.3k
views
2
answers
Comment: C: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
... I am supposed to find the gene expression level for each condition within their 8 biological replicates. You can retrieve transcript FPKMs (analogous to RPKM) by using cufflinks on the aligned reads for each condition. The aligned reads are normally saved as .bam file after the mapping procedure. B ...
written 6.2 years ago by johannes.helmuth110
5
votes
2
answers
4.3k
views
2
answers
Answer: A: Calculating Rpkm For Rna-Seq Data Including Several Samples Each Condition
... Hello narges, I assume 8 samples are sequence with the same technique (possibly the same flow cell). There are different possibilities for what you want to do. Below I explain the two most common ones: Use raw mapping counts ( e.g. count with bedtools) for calling differentially expressed genes ...
written 6.2 years ago by johannes.helmuth110
1
vote
1
answer
5.3k
views
1
answers
Answer: A: Intersectbed/Coveragebed -Split Purify Exon?
... I am confused because you talk about calculating RPKM but, with coverageBed, you do not calculate a RPKM value. Taken from the documentation, the program gives you information on 1) The number of features in A that overlapped the B interval. 2) The number of bases in B that had non-zero coverage. ...
written 6.6 years ago by johannes.helmuth110
0
votes
2
answers
5.8k
views
2
answers
Comment: C: Correlation Of Fpkm And Length Normalized Transcript Mapped Read Count
... Thanks for this thorough answer. I thought this has an effect on the expression estimate in cufflinks. Nevertheless I did not expect this disrupting the correlation so much. When using RefSeq, all transcripts of a gene a annotated and you are right that dividing by all exon lengths is not correct ...
written 6.7 years ago by johannes.helmuth110
0
votes
2
answers
5.8k
views
2
answers
Comment: C: Correlation Of Fpkm And Length Normalized Transcript Mapped Read Count
... @Istvan Albert: I use the -abam flag to provide the accepted_hits.bam file from the tophat output ...
written 6.7 years ago by johannes.helmuth110
5
votes
2
answers
5.8k
views
2
answers
Correlation Of Fpkm And Length Normalized Transcript Mapped Read Count
... Hello, in the process of estimating expression for a 16 human tissue dataset ("Human Body Map 2.0 GSE30611") I used different methods to estimate the expression of the genes. After mapping against hg19 genome version, I used the UCSC provided refseq annotation for hg19 to count mapped reads for ~40 ...
bedtools cufflinks next-gen written 6.7 years ago by johannes.helmuth110 • updated 7 months ago by Biostar ♦♦ 20

Latest awards to johannes.helmuth

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: 1202 users visited in the last hour