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i have problem in building the database manually in snpeff database
i have problem in building the database manually in snpeff database
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You need to provide additional information before people can help.
What command are you running? What error do you get (if any)? -
SNPeff database building error
java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
There might be differences in the chromosome names used in the genes file ('/home/crpgws2/Desktop/snpEff/./data/ver6/genes.gff')
and the chromosme names used in the 'reference sequence' file.
Please check that chromosome names in both files match.
I got this error while running the snpeff database building command. Should I modify my chromosome name in ref seq or I have to modify the gff file. I am doing this to create Vigna radiata reference. Please let me know what can i do to solve this problem.Comment
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Comment
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I have run SNPeff successfully. but i found some problem in html output file, as my input VCF line number and variants before filter are two different numbers. While in my view that must be same. What can be the reason for this variation although In my Input vcf and output vcf have the same no. of entries, but still the html stats varies from this number.
Summary
Genome ver6
Date 2017-04-05 11:58
SnpEff version
SnpEff 4.3k (build 2017-03-29 17:16), by Pablo Cingolani
Command line arguments
SnpEff ver6 VIGNA_SUBLOBATA_SNV.vcf
Warnings 70,058
Errors 0
Number of lines (input file) 100,273
Number of variants (before filter) 104,184
Number of not variants
(i.e. reference equals alternative) 0
Number of variants processed
(i.e. after filter and non-variants) 103,341
Number of known variants
(i.e. non-empty ID) 0 ( 0% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 1,382
Number of effects 223,468
Genome total length 463,637,892
Genome effective length 333,860,997
Variant rate 1 variant every 3,230 basesComment
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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
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