Comments (3)
The script isn't compatible with VCF format. In a future release of HISAT2, I'll modify the script to support VCF format. BTW, it is necessary that we need the same chromosome names: GRCh37 has 1, 2, 3, ... while snpCommon.txt has chr1, chr2, chr3, ...
from hisat2.
@infphilo thanks for the reply.. I guess "chr" isn't the issue in this case since I am using the snpCommons.txt from here (http://ccb.jhu.edu/software/hisat2/downloads/evaluation/data/snpCommon_22.txt), where we don't have "chr" in chromosome names.
First two lines from GRCh37_ensembl_genome.fa :
>1 dna_sm:chromosome chromosome:GRCh37:1:1:249250621:1 REF
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
However I tried to find a workaround to get the information from vcf file (since it seems in my case the snpCommons.txt is not available anyway) . I got something like this using my script:
# ID CHR TYPE POS AltBase/Length/Sequence
rs235202311 1 deletion 3010567 6
rs220682121 1 single 3010582 A
rs233361213 1 single 3010583 G
rs249503176 1 single 3010601 G
rs219761216 1 single 3010629 A
rs235606595 1 single 3010634 G
rs235822761 1 insertion 3010661 G,GGTTTT,GTT,GGTT
rs262127828 1 single 3010704 G
rs226648868 1 single 3010724 A
rs248800471 1 single 3010736 A
rs265573862 1 single 3010797 C
Do you think this will be a valid input to build the graph index?
from hisat2.
Thanks for the merge-- sorry to prematurely close this issue; this fixes one issue, but I think somewhere in hisat2-build when it is parsing the headers in the FASTA file it has a similar logic, which leads to the snps/splice sites/exons being ignored, so I think there is one more place it has to change.
from hisat2.
Related Issues (20)
- hisat2-build DOES NOT work for me! HOT 1
- building standard hisat-3n indices with --base-change but not --repeat-index HOT 4
- "Local Graph Exploded" warning for hisat2 build using --snp,--haplotype,--exon and --ss.
- Hisat2 [Errno 2] No such file or directory
- Align ATAC-seq with Hisat2?
- error minimum intron length with hisat2 v. 2.2.1
- Repeat mapping with different result
- Feature request: Add support for xz and zstd
- hisat2 hangs aligning axolotl reads HOT 1
- Output files(.snp, .haplotype) of hisat2_extract_snps_haplotypes_*.py are empty
- Please add the pbat option of hisat-3n
- A question about methylation information extraction
- Any plans to support Apple Silicon architecture? HOT 1
- Installation Issue Error 1 - make HOT 1
- -np argument seemingly not working
- ERR): "fastq file.fastq" does not exist. Exiting now ...
- [Bug Report] hisat2-align exited with value 137, space complexity of hisat2
- hisat2 location does not exist
- Hisat-3N mapping quality
- hisat2-build index for circRNA-seq
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hisat2.