User: Sam

gravatar for Sam
Sam140
Reputation:
140
Status:
Trusted
Location:
Last seen:
5 months, 2 weeks ago
Joined:
3 years, 3 months ago
Email:
V**********@gmail.com

Posts by Sam

<prev • 155 results • page 1 of 16 • next >
0
votes
1
answer
317
views
1
answers
Comment: C: Integration of RNA-Seq data with microarray data
... this paper also may be useful https://academic.oup.com/nar/article/45/17/9860/4084660 ...
written 8 months ago by Sam140
0
votes
0
answers
1.2k
views
0
answers
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 17 months ago by Sam140 • updated 15 months ago by Biostar ♦♦ 20
3
votes
1
answer
424
views
1
answer
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 18 months ago by Sam140 • updated 17 months ago by Zev.Kronenberg11k
1
vote
1
answer
433
views
1
answers
Comment: C: print non match to list lines of GTF file
... I used egrep instead of grep and it worked! ...
written 19 months ago by Sam140
5
votes
1
answer
433
views
1
answer
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 19 months ago by Sam140
5
votes
3
answers
421
views
7 follow
3
answers
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 21 months ago by Sam140 • updated 21 months ago by curious470
0
votes
1
answer
493
views
1
answers
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 23 months ago by Sam140
0
votes
1
answer
493
views
1
answers
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 23 months ago by Sam140
4
votes
1
answer
493
views
1
answer
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 23 months ago by Sam140
0
votes
1
answer
649
views
1
answers
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 23 months ago by Sam140

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 classification of small RNA-seq
Popular Question 7 months ago, created a question with more than 1,000 views. For over presented kmer in fastq
Popular Question 8 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 8 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 17 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 17 months ago, created a question with more than 1,000 views. For classification of small RNA-seq
Popular Question 17 months ago, created a question with more than 1,000 views. For miRNAs interaction networks analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For add header with awk
Popular Question 17 months ago, created a question with more than 1,000 views. For what is the easiest/fastest way to convert from BAM to GTF
Popular Question 17 months ago, created a question with more than 1,000 views. For over presented kmer in fastq
Popular Question 17 months ago, created a question with more than 1,000 views. For fastq file data
Student 17 months ago, asked a question with at least 3 up-votes. For changing the name of files
Popular Question 23 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 23 months ago, created a question with more than 1,000 views. For add header with awk
Popular Question 23 months ago, created a question with more than 1,000 views. For bash and awk code
Popular Question 2.5 years ago, created a question with more than 1,000 views. For bash and awk code
Supporter 2.7 years ago, voted at least 25 times.
Centurion 2.8 years ago, created 100 posts.
Rising Star 3.2 years ago, created 50 posts within first three months of joining.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1742 users visited in the last hour
_