Questions tagged [bowtie2]
6 questions
1
vote
1 answer
fails to direct to bowtie2 index when using snakemake
I am trying to execute this snakemake-rule:
rule test_bowtie2:
input:
idx=multiext(
"/home/databases/genomes/Homo_sapiens/rCRS/bowtieindex/rCRS",
".1.bt2",
".2.bt2",
".3.bt2",
…
MONI
- 13
- 3
1
vote
0 answers
stringtie guide reference annotation error
With bowtie2-build I have created an index file of the arabidopsis Araport11 genome (https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FAraport11_genome_release) where I have used…
max coenen
- 11
- 1
0
votes
0 answers
Index error while using OligoMiner commands in wsl
I am trying to design oligoprobes using OligoMiner tool in windows subsystem linux (wsl) by activating anaconda software. Please have a loo to th ecommands given below. in the middle i am facing an error of Index error and I am not able to fix it. I…
Rahul
- 1
0
votes
3 answers
Directory argument for Bowtie2
I'm using the software Bowtie 2 which aligns genome sequences. I have all my indexes in a directory miniReference1.
When I call Bowtie2 with the -x option I get the error that my index is not a Bowtie 2 index. What am I doing wrong? Below is a…
Raghad Shurpaje
- 11
- 1
0
votes
0 answers
Bowtie2 error : " does not exist or is not a Bowtie 2 index"
I'm very new to bioinformatics and RNA-seq so go easy on me. I keep getting the same error when I try perform my analysis. For background: I have a folder called tutorial, in the folder there are 4 other folders (important ones for now are…
egg
- 1
- 1
0
votes
0 answers
How do I fix Bowtie and Python Error (Errno2)?
I am trying to repeat the "Indexing a reference genome" step of this tutorial.
However, when I run the command
../bowtie2-master/bowtie2-build ./bowtie2-master/example/reference/lambda_virus.fa lambda_virus
This error happens:
File…
Luís Telles
- 694
- 3
- 13