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FastaAlternateReferenceMaker creates different size fasta.

fastaalternatereferencemaker snp written 9 months ago by zaibunnisa.t • 0 • updated 9 months ago by WouterDeCoster ♦ 32k

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865

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GATK FastaAlternateReferenceMaker giving error

gatk fastaalternatereferencemaker written 2.0 years ago by PAn • 20

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1.2k

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rename fasta headers in FastaAlternateReferenceMaker output

fasta bed header fastaalternatereferencemaker gatk written 2.2 years ago by mosquitoes • 0

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1.5k

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Fasta Alternate Reference Maker extracted fasta files are same as reference

gatk fastaalternatereferencemaker myposts written 3.2 years ago by nuketbilgen • 30 • updated 2.6 years ago by dsosa • 0

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2.1k

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Error when trying to fix the contigs order in the reference and vcf for FastaAlternateReferenceMaker

gatk fastaalternatereferencemaker rna-seq written 3.2 years ago by tiago211287 • 1.0k

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Recent Replies

C: Improving efficiency for a looping, mathematical script by Volka • 30
Thanks for the reply! I actually use itertools to compute all the combinations before the actual ...
A: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMto by colindaven • 800
Hi, I tried this some time ago, and found it made significant assumptions about read names. I.e. ...
A: Some Question About Hi-C data Analysis by Ashley • 10
I mapped the fastq files using bwa. I don't want to map them again.
A: STAR problem: EXITING because of INPUT ERROR: could not open genomeFastaFile: by caggtaagtat • 330
Hi, I'm not sure if that is really the problem, but there seems to be an extra empty space charac...
A: Some Question About Hi-C data Analysis by Ashley • 10
My script is that juicer.sh -d /$path/merge -s "MboI" -S final -p /$path/hg19.chrom.sizes -y /$p...
C: best practice for renaming file in CWL workflow by Michael R. Crusoe • 1.1k
`cwlexec` does support `InlineJavascriptRequirement`s so there is no compatibility issue with the...
A: best practice for renaming file in CWL workflow by Michael R. Crusoe • 1.1k
Hello ionox0, That is acceptable way to rename, yes. However, `**` is not part of the POSIX glob...
C: How to convert transcript level TPM to gene level TPM ? by i.sudbery • 2.6k
transcript_tpm is the name of the dataframe, not a column in it.
C: How to find CNV or CN state information from rawcopy output ? by pup-ccmb • 0
I have used rawcopy R-package to analyze .cell files for CNV analysis. Here, outputs generated wh...
A: references for fold-change cutoff by Fabio Marroni • 1.8k
Maybe [this][1] or [this][2] might help? [1]: https://bmcbioinformatics.biomedcentral.com/art...
C: references for fold-change cutoff by russhh • 3.9k
I don't think you need a reference. What you need is to show that your results are robust to the ...
C: Extract 1KB upstream of specific gene in X chromosome by ATpoint ♦ 8.1k
while [[ 1 > 0 ]]; do ./sarcasm.sh; done

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