User: Fawzi Yassine

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Posts by Fawzi Yassine

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Comment: C: fold change in Ballgown
... hi, The stattest doc says fc=llog(expression+1), while forums say fc=wt/ko if the groups are wt and ko. ...
written 3 days ago by Fawzi Yassine0
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Comment: A: fold change in Ballgown
... hi, The stattest doc says fc=llog(expression+1), while forums say fc=wt/ko if the groups are wt and ko. ...
written 3 days ago by Fawzi Yassine0
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fold change in Ballgown
... What is the formula that Ballgown uses to calculate fc? Does it use a log? thank you, ...
rna-seq written 6 days ago by Fawzi Yassine0
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Comment: C: ballgown has "." as Gene Names
... I solved the problem, the annotation file did not a gene_name column. ...
written 22 days ago by Fawzi Yassine0
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Answer: A: ballgown has "." as Gene Names
... I solved the problem, the annotation file did not a gene_name column. ...
written 22 days ago by Fawzi Yassine0
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Comment: C: ballgown has "." as Gene Names
... Aditi, I am sorry for the late reply. I was fixing my PC.. Below is the code for stringtie and ballgown. Here is the code for stringtie: `stringtie -e -B -p 8 -G ./stringtie_merged.gtf -o ${BALLGOWNDIR}/SRR${A}/SRR${A}.gtf ${HISAT2DIR}/SRR${A}.bam` Here is the code for ballgown #Read phenot ...
written 25 days ago by Fawzi Yassine0 • updated 22 days ago by genomax62k
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Comment: C: ballgown has "." as Gene Names
... Hi Aditi, It is not denovo assembly. he output of `indexes(ballgown_obj1)$t2` is t_id g_id 4 4 MSTRG.5 7 7 MSTRG.5 9 9 MSTRG.5 10 10 MSTRG.5 16 16 MSTRG.2 17 17 MSTRG.2 ...
written 5 weeks ago by Fawzi Yassine0 • updated 22 days ago by genomax62k
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ballgown has "." as Gene Names
... Hi, I'm using stringtie and ballgown (in R) for the standard RNA-seq data analysis. Both texp(ballgown_obj1, 'all')$gene_name and ballgown::geneNames(ballgown_obj1) return all the gene names as “.” How can I get my gene names? Thanks, ...
assembly ballgown rna-seq written 5 weeks ago by Fawzi Yassine0
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Mapping using UCSC and counting using RefSeq
... Hi, I am analyzing public RNA-seq data to find genes differentially expressed between diseased patients and controls. The paper for which the paper belong says: ” The reads were mapped to human genome (hg19) by TopHat. The number of fragments in each known gene from RefSeq database (downloaded from ...
genome assembly alignment rna-seq written 6 weeks ago by Fawzi Yassine0 • updated 6 weeks ago by David Langenberger8.7k
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Comment: C: Affymetrix Microarray data
... Thanks Spacebio, Where do I specify the databases to query (e.g. kegg, go, reactome)? Where do I specify the biological process I am looking for? regards,   ...
written 18 months ago by Fawzi Yassine0

Latest awards to Fawzi Yassine

Popular Question 3 days ago, created a question with more than 1,000 views. For Affymetrix Microarray data
Scholar 22 days ago, created an answer that has been accepted. For A: ballgown has "." as Gene Names

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