User: mhockin

gravatar for mhockin
mhockin510
Reputation:
510
Status:
Trusted
Location:
United States
Last seen:
3 years, 3 months ago
Joined:
4 years, 1 month ago
Email:
m******@gmail.com

Posts by mhockin

<prev • 7 results • page 1 of 1 • next >
0
votes
1
answer
20k
views
1
answers
Comment: C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
... Please let us know- here or wherever.  Thanks! ...
written 3.5 years ago by mhockin510
2
votes
1
answer
20k
views
1
answers
Comment: C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
... Thanks for this answer, this is more or less what I had presumed.  Even better, DESeq2 appears to work well with Salmon- I wrote a short scrip to sum to gene level from the Salmon output and generated a bunch of files appropriate for R-import and managed to get everything into DESeq2 for analysis o ...
written 3.5 years ago by mhockin510
1
vote
2
answers
1.1k
views
2
answers
Answer: A: Called variants in VCF file are mapped to untarged regions.. Does it make sense?
... Targeted or not- if your looking at exons and your seq map depth is enough to call variants accurately, I would not hesitate to call variants with confidence.  According to my understanding, Modern mapping software is sufficiently accurate that if you have a single genome in your sequencing templat ...
written 3.6 years ago by mhockin510
0
votes
1
answer
20k
views
1
answers
Comment: C: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
... I apologize I think were both saying the same thing. By summing estimated transcript counts to the gene level and then truncating to an integer I can generate data that DESeq2 should be fine with- or at least will accept as properly formatted input- are you suggesting a deeper problem with the propo ...
written 3.6 years ago by mhockin510
0
votes
1
answer
20k
views
1
answers
Comment: A: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
... Clarification- My reading of the manual for DESeq2 seems at odds with the idea that summation of "estimated" read counts would not be appropriate.  They state that you cannot use "normalized" read counts, which is not -I think- the output of Kallisto  nor Salmon (for which I am certain its not norm ...
written 3.6 years ago by mhockin510
2
votes
1
answer
20k
views
1
answers
Comment: A: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
... I will look into limma/voom but had not/have not used these tools. Both the Kallisto and Salmon manuals state that they provide estimated read counts, and in the case of Salmon it is directly stated that you can sum these to gene level for use in DESeq analysis.  I fully believe them, but as I ment ...
written 3.6 years ago by mhockin510
97
votes
1
answer
20k
views
57 follow
1
answer
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
...   I am working on analysis for an RNASeq experiment with the end goal of using DESeq2 to generate a list of differentially expressed genes.  We have 4 biological replicates for 4 conditions (differing genotypes in mice).  We have 50 bp single ended Illumina read sets, on total RNA (they had low inp ...
rnaseq deseq2 salmon deseq kallisto written 3.6 years ago by mhockin510 • updated 3.6 years ago by Michael Love1.7k

Latest awards to mhockin

Student 3.6 years ago, asked a question with at least 3 up-votes. For Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1232 users visited in the last hour