User: Sam
Sam • 130
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Posts by Sam
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... Dear Biostars
I used the vcftools with command below to calculate inbreeding coefficient (F) of a subpopulation but the number of site (N_SITES) in the output file is much less than the sites which are available in the vcf file.
The number of sites in the vcf file is about 47000 but in the output ...
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... Dear Biostars
I used the vcflib-popstats to calculate FIS of a subpopulation but I have same FIS number for positions with the different number of hets (4th column). also, which formula did it use to the calculation Fis?
would you have any idea?
Thanks
target_allele_frequency ex ...
written 12 weeks ago by
Sam • 130
• updated
9 weeks ago by
Zev.Kronenberg ♦ 11k
1
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207
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1
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... I used egrep instead of grep and it worked! ...
written 4 months ago by
Sam • 130
5
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207
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... Dear Biostars
I have a GTF file and also a gene_id list file. I want to exclude the lines contain the gene_id of list file
any help?
Thanks
GTF file:
Chr08 StringTie exon 58908449 58908806 1000 - . gene_id "MSTRG.26714"; transcript_id "MSTRG.26714.1"; exon_number "1";
Ch ...
written 4 months ago by
Sam • 130
5
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3
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259
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7 follow
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... Dear All
I have two files of gene list in tab format, I want to compare 2nd column if 1st file file with 1st column of 2nd file and report all columns in both files for each match
any help ?
Thanks
file 1
1st column 2nd column
chr10_17026 VIT_202s0033g00190
chr18_37402 VI ...
written 5 months ago by
Sam • 130
• updated
5 months ago by
brett.vanderwerff • 140
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... ok, thanks . just in case it's not also possible to distinguish between sense and antisense overlapping transcript via qPCR and primer design, right? ...
written 7 months ago by
Sam • 130
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260
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... but I can determine which strand a read maps to, right? to have a number of reads that map to sense and antisense strand. ...
written 7 months ago by
Sam • 130
4
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1
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260
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1
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... Dear All
I used unstranded RNA-seq for non-coding RNA prediction, in 1st step I removed all sequence which is overlapping (in sense) exons of the reference annotation. so can I consider the remaining reads that map to exonic antisense strand as antisense transcript?
Thanks
...
written 7 months ago by
Sam • 130
0
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284
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... featurecounts with -g transcript_id give about 20% less DE mRNAs compare to grouping according gene_id. so is it expected to have less DE in transcript level? I think if we compare transcript vs. transcript( for mRNAs vs. lncRNAs transcript correlation), it could produce more robust data. is it tr ...
written 8 months ago by
Sam • 130
1
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284
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... Dear Biostars
I predicted some lncRNAs transcript according to RNA-seq data and then I used featurecounts to count the lncRNAs transcript (-t exon and -g transcript_id ) in the BAM files. for lncRNA/mRNA co-expression analysis, should I count mRNAs according to transcipt_id or gene_id (-t exon and ...
written 8 months ago by
Sam • 130
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For Deseq2 count matrix
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created a question with more than 1,000 views.
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created 100 posts.
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created 50 posts within first three months of joining.
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