User: interfect

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interfect0
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Posts by interfect

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Comment: C: Sub-Record Indexing Of Fasta Files In Python?
... The fastahack module seems to be working great for me. It has a dependency on cython that isn't listed in its setup.py, but once I figured that out I was able to get it working very quickly. Thanks! ...
written 7.2 years ago by interfect0
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Sub-Record Indexing Of Fasta Files In Python?
... Hello, I have several genomes, each spread across multiple FASTA files. Some of these files contain multiple short sequences, and some of them contain large, chromosome-sized sequences. I need efficient random access to sequence data by FASTA record ID and sequence location (e.g. chr1:12384-12884) ...
fasta biopython written 7.2 years ago by interfect0 • updated 7.2 years ago by Matt Shirley9.4k
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Comment: C: Data_Type_Specific_Filters For Gatk Variantfiltration?
... Hello, This clears things up significantly. However, I still can't find how to apply a filter only to SNPs or only to indels. Do I need to use the JEXL expressions vc.getType() == Type.INDEL and vc.getType() == Type.SNP || vc.getType() == Type.MNP to select the appropriate kinds of variants? Is the ...
written 8.0 years ago by interfect0
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Data_Type_Specific_Filters For Gatk Variantfiltration?
... The GATK documentation for best-practices genotype calling recommends filtering called variants. Usually, you should use an adaptive filter that learns from a set of known good variants. If you do not have enough data for that (or, presumably, if you do not have a database of known variants for your ...
gatk written 8.0 years ago by interfect0 • updated 8.0 years ago by vdauwera960
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Comment: C: Clustalw Ignoring Custom Weight Matrix
... I tried both -dnamatrix and -pwdnamatrix. Neither has any effect on the output. ...
written 8.0 years ago by interfect0
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Clustalw Ignoring Custom Weight Matrix
... I'm attempting to specify a custom match/mismatch matrix for CLUSTALW 2.1 doing a pairwise DNA alignment. The program takes the matrix file and reads it, at least partially. It throws an error if the row and column labels are invalid, but not if, say, a numerical entry in the matrix is replaced with ...
matrix clustalw alignment written 8.0 years ago by interfect0 • updated 9 days ago by Biostar ♦♦ 20

Latest awards to interfect

Popular Question 6.3 years ago, created a question with more than 1,000 views. For Data_Type_Specific_Filters For Gatk Variantfiltration?
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Clustalw Ignoring Custom Weight Matrix
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Sub-Record Indexing Of Fasta Files In Python?

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