User: Kristin Muench

gravatar for Kristin Muench
Reputation:
220
Status:
Trusted
Location:
United States
Twitter:
kristin_muench
Last seen:
2 weeks, 4 days ago
Joined:
3 years, 10 months ago
Email:
k******@stanford.edu

Posts by Kristin Muench

<prev • 63 results • page 1 of 7 • next >
0
votes
0
answers
113
views
0
answers
SVA Input: Should SVs be calculated on normalized data?
... Hello, I'm trying to use SVA to calculate SVs in my DESeq2 analysis. In a couple of examples, I've seen people generate model matrices using the *raw* data, but actually calculate SVs on *normalized* data. For example, this post: https://www.biostars.org/p/201668/ Shouldn't you be using the raw d ...
R sva rna-seq written 5 weeks ago by Kristin Muench220
0
votes
1
answer
254
views
1
answers
Comment: C: Kallisto will not produce .bam files
... Aha, I see! In fact, I did see the 'bam content' in my output as you predicted, not a separate pseudoalignments.bam file: >> head kall_pipeScratch_1192561.out [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of t ...
written 8 weeks ago by Kristin Muench220
3
votes
1
answer
254
views
1
answer
Kallisto will not produce .bam files
... Hello, I'm trying to generate .bam files along with my kallisto output, as described here: https://pachterlab.github.io/kallisto/manual Unfortunately, when I run this command: kallisto quant -i $kallistoIdx -o $outputFileLoc/$sample --pseudobam -b 100 $Read1 $Read2 I only see the standar ...
kallisto rna-seq written 8 weeks ago by Kristin Muench220 • updated 8 weeks ago by Kevin Blighe21k
0
votes
2
answers
292
views
2
answers
Comment: C: Should kallisto take hours to run?
... Ah! I think I see your point. I thought the fasta files from hg19 represented a human transcriptome, but I see they represent a reference *genome*: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/ I'll re-download a human reference transcriptome and try again. Thank you! ...
written 12 weeks ago by Kristin Muench220
0
votes
2
answers
292
views
2
answers
Comment: C: Should kallisto take hours to run?
... Oops, I mistyped - you are correct. Modifying original post ...
written 12 weeks ago by Kristin Muench220
7
votes
2
answers
292
views
2
answers
Should kallisto take hours to run?
... Hello, I'm trying to align some test .fastq files to a reference using kallisto. The reference is composed of human transcriptome + a couple of plasmid sequences (~12000 characters) stored in .fa format. I generated the index using this command: humFa="/path/to/ucsc/fasta/files/RefGenomes/H_s ...
kallisto rna-seq written 12 weeks ago by Kristin Muench220
1
vote
1
answer
497
views
1
answers
Comment: C: Error in (function...) thrown by WGCNA tutorial (R)
... How odd! Thanks for the feedback. Indeed - if I'm in RStudio and it stops working, doing install.packages('WGCNA') and then library(WGCNA) usually helps. Wonder if restarting the R environment has something to do with it? Hm... ...
written 3 months ago by Kristin Muench220
7
votes
1
answer
497
views
5 follow
1
answer
Error in (function...) thrown by WGCNA tutorial (R)
... Hello, I am trying to follow along with the network generation/cluster generation part of the WGCNA tutorial: https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-blockwise.pdf I am getting the same error regardless of whether I use data ...
wgcna rna-seq R written 3 months ago by Kristin Muench220 • updated 25 days ago by wonderfulzhu198550
0
votes
0
answers
290
views
0
answers
Comment: C: Adding plasmid sequences to gtf file
... Update: it now runs, but unfortunately the alignment is taking a lot of time (5 days on the step "sorting Suffix Array chunks and saving them to disk..."). Will keep working on it, thanks! ...
written 3 months ago by Kristin Muench220
0
votes
1
answer
333
views
1
answers
Comment: C: [STAR] Why are there so many more mapped reads than unmapped reads in my .sam ou
... UPDATE: You're right - there was a step when I wasn't converting .bam to .sam appropriately. Thanks for your help! ...
written 3 months ago by Kristin Muench220

Latest awards to Kristin Muench

Popular Question 11 weeks ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Great Question 4 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Supporter 4 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For How many reads should I expect for paired end reads when coverage = 30 million?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to make lumi accept .txt data?
Popular Question 11 months ago, created a question with more than 1,000 views. For Could a "complete" RNA-Seq database feasibly exclude some protein-coding transcripts?
Popular Question 11 months ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 11 months ago, created a question with more than 1,000 views. For Is it possible to compare 3SEQ and RNA-Seq data?
Great Question 18 months ago, created a question with more than 5,000 views. For Bowtie2: Why won't it recognize my index files?
Popular Question 18 months ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Determining gene expression with 2 biological replicates and RPKM data only

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour