User: majeedaasim

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majeedaasim40
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40
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New User
Location:
United States
Last seen:
8 months, 2 weeks ago
Joined:
4 years, 11 months ago
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m**********@gmail.com

Posts by majeedaasim

<prev • 85 results • page 1 of 9 • next >
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Calculation of P2 values for finding the mutational role in codon usage bias.
... I am working on finding codon usage bias and its determining factors in my species. Foe calculating P2 I have confusion. P2 = (WWC+SSU)/(WWY+SSY) where W = A or T, S = C or G and Y = C or T I have values of A,T,G,C Now when I put the value of W, I am confused whether to put A or T. I mean do I h ...
codon usage bias p2 mutatioin written 8 months ago by majeedaasim40
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Answer: A: Problem in running STAR
... I solved it by using the parameter --genomeChrBinNbits = 11 The number here depends on the number of sacffolds/sequences and assembly size and is calculated by using the formula given in the manual as min(18,log2[max(GenomeLength/NumberOfReferences,ReadLength)]) ...
written 19 months ago by majeedaasim40
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Comment: C: Problem in running STAR
... I just installed it with conda ...
written 19 months ago by majeedaasim40
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Comment: A: Problem in running STAR
... I cleared the cache, after that the memory status is MemTotal: 65702032 kB MemFree: 61628952 kB MemAvailable: 62446420 kB Buffers: 106076 kB Cached: 1312752 kB SwapCached: 0 kB Active: 2998420 kB Inactive: ...
written 19 months ago by majeedaasim40
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Comment: A: Problem in running STAR
... It gives following information > aasim@aasim-ProLiant-ML150-Gen9:~$ cat /proc/meminfo MemTotal: 65702032 kB MemFree: 30549880 kB MemAvailable: 62552108 kB Buffers: 571404 kB Cached: 31485836 kB SwapCached: 0 kB Active: ...
written 19 months ago by majeedaasim40 • updated 19 months ago by WouterDeCoster44k
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Problem in running STAR
... I am using STAR 2.5.3a on my system for aligning my Fasta sequences. THe command I used is aasim@aasim-ProLiant-ML150-Gen9:~/Aasim/bin/STAR-2.5.3a/star_index$ STAR --runMode genomeGenerate --runThreadN 24 --genomeDir index --genomeFastaFiles Concatenate_master_assembly.fasta --limitGenomeGene ...
rnaseq star written 19 months ago by majeedaasim40
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Comment: C: how to reorder lines in afile based on a list of gene IDS?
... I want solution in R ...
written 23 months ago by majeedaasim40
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how to reorder lines in afile based on a list of gene IDS?
... I have two files; File one: ID SCORE PVALUE A 1 0.1 B 2 0.2 C 3 0.3 D 4 0.4 FIle 2: ID C B A Now I want to reorder my file 1, in the sequence as present in file 2. THanks ...
reorder written 23 months ago by majeedaasim40
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How to extract gene IDs from a tabular file based on a list of locus tags?
... I have a file like: GeneID Locus tag Protein name 839580 AT1G01010 NAC domain containing protein 1 839569 AT1G01020 ARV1 family protein 839569 AT1G01020 ARV1 family protein 839569 AT1G01020 ARV1 family protein I also have a list of locus tags (arround 5000) which I want to extract from the ...
R written 23 months ago by majeedaasim40 • updated 23 months ago by Alex Reynolds30k
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Comment: C: problem in trinity differential gene expression protocol
... When I triued to install it from bioconductor using source("https://bioconductor.org/biocLite.R") biocLite("edgeR") It gives along list of errors like: /usr/bin/locale:88:20: error: stray '\10' in program /usr/bin/locale:89:1: error: stray '\16' in program /usr/bin/locale:89 ...
written 23 months ago by majeedaasim40 • updated 23 months ago by RamRS28k

Latest awards to majeedaasim

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Scholar 19 months ago, created an answer that has been accepted. For A: Problem in running STAR
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