User: williamsbrian5064

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Posts by williamsbrian5064

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Comment: C: How to remove contamination from WGS fastq files
... Also, does bbsplit give you a file that contains the clean reads and another file that contains the contaminated reads? If it doesn't I guess I could just run it twice, one with our species, and the second with the human genome ...
written 8 weeks ago by williamsbrian5064290
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Comment: C: How to remove contamination from WGS fastq files
... Thank you for your response! We think it happened at the sequencing provider we just aren't sure how we can really prove that. Do you know of any way to prove that? ...
written 8 weeks ago by williamsbrian5064290
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Comment: C: How to remove contamination from WGS fastq files
... I think I'll try both methods and see how it goes. Thank you for your suggestions ...
written 8 weeks ago by williamsbrian5064290
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Comment: C: How to remove contamination from WGS fastq files
... Huh.. that is an interesting idea? How would you remove the reads that map against the human genome? ...
written 8 weeks ago by williamsbrian5064290
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How to remove contamination from WGS fastq files
... Hi, I recently got back some fastq files. The samples I sent off for sequencing appear to have some human DNA in them. I was wondering if there was a way to remove the human DNA from my samples. The fastq files are 150 bp paired-end reads. I saw there were some post suggestion bbsplit and other sug ...
next-gen sequence written 8 weeks ago by williamsbrian5064290 • updated 8 weeks ago by genomax92k
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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 14 months ago by williamsbrian5064290
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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 14 months ago by williamsbrian5064290
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Comment: C: Best tool for variant calling
... It might be worth creating your own question. Seem rather specific. ...
written 14 months ago by williamsbrian5064290
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Comment: C: Issues generating bcf file with samtools
... I guess I will give that a try. I am aware! ...
written 16 months ago by williamsbrian5064290
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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 16 months ago by williamsbrian5064290

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