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Recent Replies
Comment: No variant in the Pseudoautosomal regions of gomad chrY ?
by
Pierre Lindenbaum
166k
Ah, somehow your answer is right, in the reference the PAR on chrY is masked:
$ samtools faidx red.fasta "chrY:10001-2781479" | tail …
Comment: How to extract specific chromosome from vcf file
by
Reza
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0
Perhaps something like this is more compact:
vcftools --gzvcf <file.vcf.gz> $( seq -f "--chr %g" 1 23 ) --recode --out subset_chr1-23
Comment: No variant in the Pseudoautosomal regions of gomad chrY ?
by
GenoMax
151k
Will delete then. See if you get any good answers directly. Most of the papers that GPT used as source appear to be older (~ mid-2000s).
Comment: No variant in the Pseudoautosomal regions of gomad chrY ?
by
Pierre Lindenbaum
166k
@genomax yeah, I asked GPT too but I don't think it's right (?). The reads are mapped using bwa so even if the regions are similar between…
Answer: No variant in the Pseudoautosomal regions of gomad chrY ?
by
GenoMax
151k
GPT says the following. Until we get an answer this seems logical.
There *are* actually variants in the pseudoautosomal regions (PARs) of …
Comment: How to generate identiy score between aligned sequences with Mauve?
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marongiu.luigi
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740
Thank you, I used `[skani][1]` but it requires the build a model of several genomes together. Can I use it for only two genomes?
[1]: …
Comment: How to generate identiy score between aligned sequences with Mauve?
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marongiu.luigi
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Thank you, I ran with `progressiveMauve --weight=15 --output=./out_file.mauve chr1.fa` where `chr1.fa` is a multifasta with the two genomes…
Answer: Genomic Data Portal (GDC) download a given a link file
by
bioinformagician
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Solved using this, then merging all maf files into one. But would like a solution to download that one in specific just to check if it is t…
Comment: How to generate identiy score between aligned sequences with Mauve?
by
GenoMax
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According to the manual a file is supposed to be produced by Mauve: https://darlinglab.org/mauve/user-guide/files.html#:~:text=The%20identi…
Answer: How to generate identiy score between aligned sequences with Mauve?
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GenoMax
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`FastANI` has bee recommended by users here for this type of comparison (since you are mentioning `Mauve` you are likely referring to genom…
Comment: Cosmic database update issue in annovar
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Ahmed
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Ensure that the cosmic input files are not compressed. Also, Try using following prepare_annovar_user.pl:
`http://www.openbioinformatics.o…
Answer: Cluster annotation in single cell
by
Shiyang
•
0
I'd like to recommend a new tool called **mLLMCelltype** that can greatly simplify the cluster annotation process for single-cell RNA-seq d…
Comment: Interpretation of the results: PCA
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rfran010
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I would say exact interpretations depend more on the nature of the data, experimental setup, and data processing steps. You provided some g…
Answer: Finding matched RNA-seq and Ribo-seq datasets for Nicotiana benthamiana under th
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colindaven
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This might be very tricky.
Try here
https://sra-explorer.info/
Search for:
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colindaven
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HiSat is another RNA-seq aligner which uses less RAM.
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