User: thjnant

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thjnant90
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90
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New User
Location:
Germany
Last seen:
3 years, 9 months ago
Joined:
5 years, 6 months ago
Email:
t******@gmail.com

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Posts by thjnant

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Learn perl or python for bioinformatics?
... Thanks a lot! ...
written 3.8 years ago by thjnant90
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(Closed) Learn perl or python for bioinformatics?
... Hello, I know this is a repeated question but I would like to have new opinions on it as time changes preferences. I am about to finish the first year of my PhD studies in evolutionary genetics. I have a biology background. During this first year, I have tried to learn a bit of everything, from C t ...
perl python written 3.8 years ago by thjnant90 • updated 3.8 years ago by mxs530
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Comment: C: SNP calling from pooled RNA-seq data
... Oh, yes, you are right. As one allele may not be expressed, so, then the truly heterozygote position will be called as a homozygote. Well, I should handle the limitations. Thanks again. ...
written 4.4 years ago by thjnant90
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Comment: C: SNP calling from pooled RNA-seq data
... Thanks for your comment. From individually sequenced RNA-seq data is possible to see whether an individual is homozygote or heterozygote for a given position especially one can always check the bam files against the reference. But as you said, knowing whether a position is homozygote or heterozygote ...
written 4.4 years ago by thjnant90
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SNP calling from pooled RNA-seq data
... Hello, I need to call SNPs from pooled RNA-seq data. In each pool, I have 2 or 3 individuals. I am following the GATK pipeline for this purpose. What I wonder about, and this could be due to my lack of understanding of the SNP calling process from pooled data, if for a given position, one sees two ...
rna-seq snp written 4.4 years ago by thjnant90 • updated 4.4 years ago by Khader Shameer18k
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Comment: C: Dealing with assembly versions
... Such great help! Thank you very much. ...
written 4.4 years ago by thjnant90
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Dealing with assembly versions
... Hello, I have a set of genes of chicken but the IDs belong to an older version of chicken assembly, however now I am using galgal4 and I see several of the IDs, the names have changed. For example when I search one gene I get this message: Ensembl gene ENSGALG00000008643 is no longer in the datab ...
assembly written 4.4 years ago by thjnant90 • updated 4.4 years ago by Emily_Ensembl18k
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Investigating a genome assembly
... Hello, I have to work with a genome assembly which consists of about 32000 scaffolds (obviously, the scaffolds are not annotated) as a reference for SNP calling. However, before proceeding further, I would like to: 1. Read about the process of making a genome assembly. 2. Get basic statistics of ...
assembly written 4.4 years ago by thjnant90 • updated 4.4 years ago by Prakki Rama2.2k
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Comment: C: Convert Illumina 1.5 to Illumina 1.8
... I found this solution: sed -e '4~4y/@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghi/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJ/' myfile.fastq # add -i to save the result to the same input file   ...
written 4.4 years ago by thjnant90
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Convert Illumina 1.5 to Illumina 1.8
... Hello, I have paired end RNA-seq fastq files that has the quality score of the earlier version of Illumina, such as Illumina 1.5. I need to convert their quality scores to the one of Illumina 1.8. I was wondering if there is any script available for this purpose before I start on it myself. Thank ...
illumina quality score fastq written 4.4 years ago by thjnant90 • updated 4.4 years ago by Docroberson30

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Problem with blastp when blasting against custom made database

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