User: williamsbrian5064

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Posts by williamsbrian5064

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Comment: C: No alias or index file found for protein database
... I added a comment below if you were curious about how I resolved this problem! Thank you so much for your help, I really appreciate the time you and lieven.sterck took to help me. ...
written 8 months ago by williamsbrian5064250
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Comment: C: No alias or index file found for protein database
... I am not sure the best way to reach the two of you. I just wanted to thank you two for your help. I was able to figure this problem out (I had to put this project on the back burner). So what I did was user `conda` to download BLAST and CD-HIT. I figured that would simplify things, I noticed that I ...
written 8 months ago by williamsbrian5064250
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Comment: C: Best tool for variant calling
... It might be worth creating your own question. Seem rather specific. ...
written 8 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... I guess I will give that a try. I am aware! ...
written 10 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... I noticed that there was an extra number added to the read group. It said @RG\tID:C04893_S47_0001\tSM:C04893\tPL:illumina\tLB:C04893_lib1\tPU:barcode_C048937 but it should be @RG\tID:C04893_S47_0001\tSM:C04893\tPL:illumina\tLB:C04893_lib1\tPU:barcode_C04893 Do you think that could be t ...
written 10 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... I think it can be in bcf format? [Link][1] "-o, --output FILE Write pileup or VCF/BCF output to FILE, rather than the default of standard output" Regardless, I am not sure why this method has worked with other samples but not this particular sample. I am really trying to figure out what the issue ...
written 10 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... I can give bcftools a try but I am still not sure why I was able to get all my other samples to run. When I run the following samtools mpileup --output-tags DP,DV,DPR,INFO/DPR,DP4,SP -u -f Felis_catus.Felis_catus_9.0.dna_sm.toplevel.fa --BCF C04893_L001.sorted.dedup.bam > C04893.bcf I sti ...
written 10 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... bwa mem -M -t 16 -R '@RG\tID:C04893_S47_0001\tSM:C04893\tPL:illumina\tLB:C04893_lib1\tPU:barcode_C048937' Felis_catus.Felis_catus_9.0.dna_sm.toplevel.fa C04893_R1_001.trim.paired.fastq.gz C04893_R2_001.trim.paired.fastq.gz > C04893_001_aligned.sam java -jar -Xmx8g -Djava.io.tmpdir=tmp_C0 ...
written 10 months ago by williamsbrian5064250
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Comment: C: Issues generating bcf file with samtools
... Sorry, when I go to generate the bcf file, there is just no output. I the size of the file stays at 0 ...
written 10 months ago by williamsbrian5064250
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samtools having to use -A input option
... Hi, I am using samtools to make a bcf file and then a vcf file. I am using the following code samtools mpileup --redo-BAQ --min-BQ 30 --per-sample-mF -C 50 --output-tags DP,DV,DPR,INFO/DPR,DP4,SP -A -u -f Felis_catus.Felis_catus_9.0.dna_sm.toplevel.fa --BCF C04893_L001.sorted.dedup.bam > C ...
genome assembly next-gen alignment written 10 months ago by williamsbrian5064250

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