User: Sam

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Sam110
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1 year, 8 months ago
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Posts by Sam

<prev • 152 results • page 1 of 16 • next >
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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 10 days ago by Sam110
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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 11 days ago by Sam110
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7 follow
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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 7 weeks ago by Sam110 • updated 7 weeks ago by brett.vanderwerff120
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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 3 months ago by Sam110
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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 3 months ago by Sam110
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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 3 months ago by Sam110
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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 4 months ago by Sam110
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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 4 months ago by Sam110
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co-expression output format(rcorr.adjust)
... Dear All I want use "rcorr.adjust" (https://rdrr.io/cran/RcmdrMisc/man/rcorr.adjust.html) for gene co-expression analysis but I want to have a the output in one table contain rows , columns name , correlation , P-value and adjust P any help? output of rcorr.adjust : ...
R co-expression written 4 months ago by Sam110 • updated 4 months ago by zx87547.5k
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(Closed) retrieve lines with bash/awk
... Dear All I have a table in this format (sep="\t"): > head (final_results) row column cor p 1 Eucgr.A00001.v2.0 Eucgr.A00003.v2.0 0.19259162 0.548714973 2 Eucgr.A00001.v2.0 Eucgr.A00004.v2.0 0.73894587 0.006039257 3 Eucgr.A00003. ...
awk bash written 4 months ago by Sam110

Latest awards to Sam

Popular Question 3 months ago, created a question with more than 1,000 views. For Deseq2 count matrix
Popular Question 3 months ago, created a question with more than 1,000 views. For add header with awk
Popular Question 3 months ago, created a question with more than 1,000 views. For bash and awk code
Popular Question 10 months ago, created a question with more than 1,000 views. For bash and awk code
Supporter 13 months ago, voted at least 25 times.
Centurion 14 months ago, created 100 posts.
Rising Star 19 months ago, created 50 posts within first three months of joining.

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