User: joomi

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joomi0
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Posts by joomi

<prev • 11 results • page 1 of 2 • next >
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Comment: A: diffSplice: Error in exon.genes[o, , drop = FALSE] : incorrect number of dimensi
... Was this solved, I have a similar issue? ...
written 7 weeks ago by joomi0
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Comment: C: bwa is getting stuck
... Thank you so much! I subsetted the two reads with zcat and ran bwa. It completed within minutes! My original files are around 7.4G in size and contain around 21959218 reads. This is for the species Zea Mays and in all of my runs I have used around 60G which is 64G/63g is the maximum that I have acce ...
written 9 months ago by joomi0
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Comment: C: bwa is getting stuck
... Hello, I don't have a log file. I have an standard output file and standard error file. The standard output looks like this: ========================================== SLURM_JOB_ID = 7116608 SLURM_NODELIST = c9-68 ========================================== and the standard error ...
written 9 months ago by joomi0
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Comment: C: bwa is getting stuck
... Hello, I should have mentioned that I already redirect to a sam file! Sorry about that. My main issue is that all my scripts are timing out. I've been running them for 24 hours and they end up stuck at the point in the standard error files. I'm not sure why it is so slow. Is this normal? How many d ...
written 9 months ago by joomi0
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Comment: A: bwa is getting stuck
... Hello, I should have mentioned that I already redirect to a sam file! Sorry about that. My main issue is that all my scripts are timing out. I've been running them for 24 hours and they end up stuck at the point in the standard error files. I'm not sure why it is so slow. Is this normal? How many ...
written 9 months ago by joomi0
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bwa is getting stuck
... Hello, I've been running bwa mem to do pair wise alignment to a reference. I have already indexed my reference and it resulted in 5 output files with the following extensions: .pac, .sa, .amb, .ann, .bwt. I have run bwa men with 60G multiple times now and all the jobs never finish. They take over ...
mem alignment bwa rna-seq written 9 months ago by joomi0
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Comment: C: How do I filter my VCF file to only include certain coordinates from a BED file?
... Thank you very much!! ...
written 12 months ago by joomi0
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How do I filter my VCF file to only include certain coordinates from a BED file?
... Hello, I have a VCF file and a BED file in the form of . How do I filter my VCF file to include SNPs that are within the coordinates of the BED file? Thank you!! ...
rna-seq snp written 12 months ago by joomi0 • updated 12 months ago by cmdcolin1.2k
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VCFtools --exclude-bed Does it include from the BED file or exclude only?
... Hello, I have a question about VCFtools --exclude-bed. I have a bed file that contains and coordinates. However I want to filter my VCF files to only contain those coordinates in the bed file I have made. I know I have to use --exclude-bed however online it is mentioned constantly that --exclud ...
rna-seq written 12 months ago by joomi0
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Comment: A: How can I make GATK fasta alternate reference maker faster
... Thank you for responding!! I'm using the following command: srun java -jar /share/apps/GATK-3.6/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -V $Files/PT_sanger2yTCA454RNvsB73_with_read_groups_filtered_refina2_snps.ann.gatk.vcf -R $Files/Zea_mays.AGPv3.22.dna.genome.fa -L $Files_made/ ...
written 12 months ago by joomi0 • updated 12 months ago by genomax70k

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