User: maximilian.mayerhofer

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Posts by maximilian.mayerhofer

<prev • 27 results • page 1 of 3 • next >
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Comment: C: bcftools breaks in for loop
... Jep, was a version issue. ...
written 3 months ago by maximilian.mayerhofer20
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[solved]bcftools breaks in for loop
... I want to filter my bcf files for various criteria. If I use it on one single file, it works, but as soon as I for-loop it, it breaks with unknown command. for n in /Volumes/Temp/PBI_CNV/results/*.bcf; do bcftools filter -i 'MAPQ>40' $n > ${n%*.bcf}_mapq.vcf done ...
vcf bcftools bash bcf for-loop written 3 months ago by maximilian.mayerhofer20
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Comment: C: DELLY CNV Calling
... Thanks! How do I specify the exclusion argument? Everything except Chr17? ...
written 4 months ago by maximilian.mayerhofer20
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DELLY CNV Calling
... So, I have to call CNVs of various bam-files using delly. Due to the rather low documentation, I am stuck. I have a genomic reference file (Homo_sapiens.GRCh38.dna.chromosome.17.fa) as well as the ref-index file (.fa.fai), an input file (HG00512.CHS.sorted.bam) and bam-index (HG00512.CHS.sorted.bam ...
delly cnv written 4 months ago by maximilian.mayerhofer20 • updated 4 months ago by Pierre Lindenbaum121k
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Comment: C: Virtual Alignment program?
... Of course, my question is: is there a pipeline/program that can do that for me? Or do I have to do this by hand? ...
written 15 months ago by maximilian.mayerhofer20
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Virtual Alignment program?
... Hello, I need to do an alignment like in the picture ![alignment][1] Is there a way to do that automatically ? Currently, I am using MAFFT to align the sequences and then Jalview to view them - do you know of a program to produce alignments like this? Best regards [1]: https://www.researchg ...
sequence alignment written 15 months ago by maximilian.mayerhofer20
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Answer: A: Blast Output not in correct dir
... So, since that seemed to be a bug, I used the following workaround: blastn -query $F -db ../database/blastdb/dbGOI.fasta -outfmt 5 >> ../output/results.xml since I used cat to put all theoutput files together, I save a line of code. ...
written 15 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... Jep, I tried full path, relative path or no path at all but everytime ( also with no specific path) it gets put into the genomes dir. ...
written 15 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... even with the ".." it isnt outputting it correctly. ...
written 15 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... problem is, even if I am in the script dir, the blast result are put into the genomes dir and not in the output dir. ...
written 15 months ago by maximilian.mayerhofer20

Latest awards to maximilian.mayerhofer

Popular Question 15 months ago, created a question with more than 1,000 views. For Extracting specific IDs + sequence from multifasta
Scholar 15 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 17 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 17 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta

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