User: Sam
Sam • 110
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Posts by Sam
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... I used egrep instead of grep and it worked! ...
written 10 days ago by
Sam • 110
5
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1
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111
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1
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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 11 days ago by
Sam • 110
5
votes
3
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193
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7 follow
3
answers
... 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 7 weeks ago by
Sam • 110
• updated
7 weeks ago by
brett.vanderwerff • 120
0
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191
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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 3 months ago by
Sam • 110
0
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1
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191
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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 3 months ago by
Sam • 110
4
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1
answer
191
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1
answer
... 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 3 months ago by
Sam • 110
0
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1
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185
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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 4 months ago by
Sam • 110
1
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1
answer
185
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1
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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 4 months ago by
Sam • 110
2
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1
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153
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1
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... 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 :
...
0
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90
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... 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. ...
written 4 months ago by
Sam • 110
Latest awards to Sam
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Deseq2 count matrix
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created a question with more than 1,000 views.
For add header with awk
Popular Question
10 months ago,
created a question with more than 1,000 views.
For bash and awk code
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voted at least 25 times.
Centurion
14 months ago,
created 100 posts.
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19 months ago,
created 50 posts within first three months of joining.
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