User: mfahim

gravatar for mfahim
mfahim10
Reputation:
10
Status:
New User
Location:
Korea, Republic Of
Scholar ID:
Google Scholar Page
Last seen:
4 years, 3 months ago
Joined:
4 years, 7 months ago
Email:
m*****@aup.edu.pk

Posts by mfahim

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Program For Flagging Alternative Splicing Events From A Genome Annotation
... did you find anything for plants?.. ...
written 4.3 years ago by mfahim10
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Comment: C: design primer for alternative splicing events
... Hi Pengchy. Could you resolve the issue?. I am facing a similar issue.. I need to design primers to differentiate various novel isoforms from the constitutive ones in Arabidopsis. What would you recommend?. ...
written 4.4 years ago by mfahim10
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Sequences of isoforms of a gene from RNAseq data
... I have finished pair-end RNAseq analysis using Tuxedo Protocol. Now I need to extract sequences of different isoforms of a gene from my samples (a total of 6). How should I proceed?. I guess I have to use *.bam, *.gtf files but how.?   I tried Genomicfeatures in R but it gets complicated for Ara ...
novel transcripts isoforms rna-seq written 4.4 years ago by mfahim10
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Comment: C: Problem installing cummeRbund in Ubuntu
... Hi FMS Gviz is not loaded.. that's the latest error I am getting. ``` Loading required package: Gviz Loading required package: grid Error : objects 'metadata', 'isTRUEorFALSE', 'isSingleString' are not exported by 'namespace:IRanges' Error: package 'Gviz' could not be loaded ``` here is my sessio ...
written 4.4 years ago by mfahim10 • updated 4 weeks ago by RamRS25k
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Comment: C: Problem installing cummeRbund in Ubuntu
... Thanks.. Will have a look at the tread.. the command sudo apt-get install libxml2 libcurl libxml2-dev did not help.. :( Cheers ...
written 4.4 years ago by mfahim10 • updated 4 weeks ago by RamRS25k
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Problem installing cummeRbund in Ubuntu
... Hi There, I am facing the following error while installing cummeRbund in Ubuntu 15 vivid.. Please help me out.. Thanks :) installing to /home/fahimish/R/x86_64-pc-linux-gnu-library/3.2/GenomicAlignments/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** ...
ubuntu cummerbund written 4.4 years ago by mfahim10 • updated 4.1 years ago by Biostar ♦♦ 20
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Comment: C: q-value is not as robust. Here is why.. or am I wrong?
... Spot on Sam..That's exactly the situation I am in. And this is affecting my volcano plots.. Can you please advise how should I plot my data or analyze it. ...
written 4.5 years ago by mfahim10 • updated 4 weeks ago by RamRS25k
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Comment: C: Volcano Plot Of Significantly Differential Exp Genes
... Hi Neil, Could you update the thread.. did you get help on this?   ...
written 4.5 years ago by mfahim10
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Comment: C: q-value is not as robust. Here is why.. or am I wrong?
... Sam, I tried posting picture with it.. but could not find attachment thingy here.. here is the same post on seqanswers.. There is a huge difference between WT and mutants.. check it out and kindly comment.. also let me know a bit more about qqplot and how it is plotted and where... I am a biologist ...
written 4.5 years ago by mfahim10
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q-value is not as robust. Here is why.. or am I wrong?
... I have four subjects at two different conditions (a total of 8 samples).. cuffdiff tells me there is no significant difference based on adjusted p-value (aka q-value). This is why I guess q-value is just overrated.. and is not applicable to every RNAseq analysis.   What do you say? ...
adjusted p cummerbund cuffdiff q-value q value written 4.5 years ago by mfahim10 • updated 4.5 years ago by Devon Ryan93k

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