User: evelyn

gravatar for evelyn
evelyn90
Reputation:
90
Status:
Trusted
Location:
Last seen:
22 hours ago
Joined:
1 year, 1 month ago
Email:
t*******@gmail.com

Posts by evelyn

<prev • 186 results • page 2 of 19 • next >
0
votes
2
answers
91
views
2
answers
RNA read alignment using transcriptome
... Hello, I want to align RNA reads to indexed reference transcriptome. But I could not find a way to make a transcriptome reference index and align using that with `hisat2`. Is the command line same for reference genome or transcriptome for hisat2. Thank you! ...
sequencing written 4 days ago by evelyn90 • updated 4 days ago by ATpoint31k
0
votes
0
answers
72
views
0
answers
Comment: C: salmon light weight alignment mode
... I am not going to remove the duplicates. I am looking for a way to use salmon alignment for sorted bam files created with hisat2 including the reference genome. ...
written 4 days ago by evelyn90
0
votes
0
answers
72
views
0
answers
Comment: C: salmon light weight alignment mode
... Thank you! I want to see any difference using this approach as compared to using fastq files. I could not find an option for light weight alignment in the documentation. ...
written 5 days ago by evelyn90
0
votes
0
answers
72
views
0
answers
salmon light weight alignment mode
... Hello, I have sorted bam files for paired end `RNA` seq fastq files using `Hisat2`, `Picard` and I want to use `salmon` alignment mode: hisat2 -q -x genome -1 input_1.fastq -2 input_2.fastq -S out.sam samtools view -bS out.sam > out.bam samtools sort out.bam -o out.sorted.bam sa ...
sequencing written 5 days ago by evelyn90
0
votes
0
answers
91
views
0
answers
Comment: C: tximport to dseq2 error
... Thank you, > rownames(samples) [1] "1" "2" "3" "4" "5" "6" > colnames(txi) NULL ...
written 10 days ago by evelyn90
0
votes
1
answer
216
views
1
answers
Comment: C: salmon to tximport error
... Thank you! I did it and got: 'select()' returned 1:1 mapping between keys and columns Is it normal? ...
written 10 days ago by evelyn90
0
votes
1
answer
216
views
1
answers
Comment: C: salmon to tximport error
... I finally got >all(file.exists(my.files)) TRUE Now I am trying to create tx2gene using: TxDb <- makeTxDbFromGFF(file = "/path/gene_models.gff") k <- keys(TxDb, keytype = "TXNAME") tx2gene <- select(TxDb, k, "GENEID", "TXNAME") head(tx2gene) But I got error ...
written 11 days ago by evelyn90
0
votes
1
answer
216
views
1
answers
Comment: C: salmon to tximport error
... Thank you! As I said above I think there might be a problem as I ran salmon for multiple files together and have only one quant.sf. Now I am trying to run an array to produce different quant.sf files for each pair of files. ...
written 11 days ago by evelyn90
0
votes
1
answer
216
views
1
answers
Comment: C: salmon to tximport error
... Okay. I ran salmon for multiple files together and have one quant.sf. Do I need to run it individually for each paired end fastq file. ...
written 11 days ago by evelyn90
0
votes
1
answer
216
views
1
answers
Comment: C: salmon to tximport error
... Okay, so in the first step after setting the path to directory containing `quant.sf,` `list.files()` just gives the names of the folders in that directories with one folder having `quant.sf` file. ...
written 11 days ago by evelyn90

Latest awards to evelyn

Popular Question 7 weeks ago, created a question with more than 1,000 views. For basename: missing operand
Supporter 4 months ago, voted at least 25 times.
Centurion 5 months ago, created 100 posts.
Scholar 8 months ago, created an answer that has been accepted. For C: Fastq to BAM

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1015 users visited in the last hour