User: Sam

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Sam130
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Posts by Sam

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inbreeding coefficient (F) with vcftools
... 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 ...
vcftools written 7 weeks ago by Sam130 • updated 11 days ago by Biostar ♦♦ 20
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vcflib-popstats to calculate FIS of a subpopulation
... 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 ...
vcflib popstats written 12 weeks ago by Sam130 • updated 9 weeks ago by Zev.Kronenberg11k
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Comment: C: print non match to list lines of GTF file
... I used egrep instead of grep and it worked! ...
written 4 months ago by Sam130
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print non match to list lines of GTF file
... 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 ...
grep bash awk written 4 months ago by Sam130
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compare two columns of two files
... 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 ...
awk bash written 5 months ago by Sam130 • updated 5 months ago by brett.vanderwerff140
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Comment: C: unstranded RNA-seq lib for ncRNA prediction
... 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 Sam130
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Comment: C: unstranded RNA-seq lib for ncRNA prediction
... 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 Sam130
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unstranded RNA-seq lib for ncRNA prediction
... 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 ...
rna-seq lncrna written 7 months ago by Sam130
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Comment: C: featurecounts flags for lncRNA and mRNA co-expression
... 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 Sam130
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featurecounts flags for lncRNA and mRNA co-expression
... 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 ...
co-expression featurecounts written 8 months ago by Sam130

Latest awards to Sam

Popular Question 7 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 7 months ago, created a question with more than 1,000 views. For add header with awk
Popular Question 7 months ago, created a question with more than 1,000 views. For bash and awk code
Popular Question 14 months ago, created a question with more than 1,000 views. For bash and awk code
Supporter 17 months ago, voted at least 25 times.
Centurion 18 months ago, created 100 posts.
Rising Star 23 months ago, created 50 posts within first three months of joining.

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