User: Giovanni.madrigal12

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Posts by Giovanni.madrigal12

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to merge multiple VCF files (each has multiple samples genotype) from differ
... More details on what commands you are using and errors would be helpful. I am aware of another post with the same issue [Merge individual vcf files][1]. There is also another tool kit called vcflib (https://github.com/vcflib/vcflib) if you would care to test your data there. [1]: http://seqanswe ...
written 9 days ago by Giovanni.madrigal1220
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Comment: C: How meaningful is GO term enrichment of SNP outliers when only a small proportio
... I don't know if this is relevant at this point in time, but it is to my knowledge that RAD-seq may not be appropriate for GO term analysis. RAD-seq is used to generate genomic data, not transcriptomic data. Genomic data does not necessarily reflect what genes an organism is expressing. In short, RAD ...
written 9 days ago by Giovanni.madrigal1220
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Comment: C: How to merge multiple VCF files (each has multiple samples genotype) from differ
... Have you already looked into VCFtools? I believe their merging, comparing, and consensus options may be beneficial. ...
written 9 days ago by Giovanni.madrigal1220
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Answer: A: How to proceed after Trinotate?
... You may consider predicting GO terms for your transcripts or evaluating the completeness of your transcriptome using BUSCO (https://busco.ezlab.org/). Additional details of your experiment (e.g. species of interest) may aid in getting better advice on this subject. ...
written 9 days ago by Giovanni.madrigal1220
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Comment: C: How to gene functional annotation ?
... You may consider using PANTHER or DAVID in order to find your GO terms for your accession names. ...
written 5 months ago by Giovanni.madrigal1220
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Comment: C: Multisample VCF file to Structure file format ?
... Thank you very much! That seemed to do the trick. You have saved me a lot of time and headache. I appreciate your help. ...
written 6 months ago by Giovanni.madrigal1220
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Comment: C: Multisample VCF file to Structure file format ?
... Thank you for the response. I have replaced the "." with zeros within the POS column; however, I am now receiving this error: Error: Line 2 of .vcf file has an invalid GT field. Looking at the head of the file through the terminal is a bit difficult due to the top row being crunched up, but in a sp ...
written 6 months ago by Giovanni.madrigal1220
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Comment: C: Multisample VCF file to Structure file format ?
... Hello chrchang523, I know that it has been quite a while since this post, but I am trying to run this method with my vcf file; however, I keep getting an error: Error: Invalid bp coordinate on line 1 of .bim file. I removed the logical information from the original vcf file as a means of improvin ...
written 6 months ago by Giovanni.madrigal1220
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Comment: C: DiscoSNP-RAD: using 1SNP_by_cluster.py
... I am also having this same problem. Please let me know if you find a solution to this issue. Thank you in advance! Sincerely, Gio ...
written 8 months ago by Giovanni.madrigal1220
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Makeblastdb Issue Buffer Overflow
... I am running into a makeblastdb issue. The error I am receiving is: *** buffer overflow detected ***: makeblastdb terminated ======= Backtrace: ========= I do not know what the issue is. I have run this program with other fasta files and had no issues with it. Here is the command I am running along ...
fasta database blast written 8 months ago by Giovanni.madrigal1220 • updated 8 months ago by genomax59k

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