User: nitinnarwade1504

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Posts by nitinnarwade1504

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Downloading all Helix-turn-helix motif containing protein from bacteria
... There is one github repository which may help you. But it may need some or more programming and or the data processing. Ex: You will get PFAM <=> UniProt id mapping along with subregions (i.e. domain region) information from the repository. You can download all the sequences using UniPort i ...
written 11 days ago by nitinnarwade1504200
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... This thread may help you....!! ...
written 11 days ago by nitinnarwade1504200
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Comment: C: Using xdformat on fasta from REPBASE returns erorr.
... I think this error is not with your `xdformat` program, your input sequence is having some ambiguous characters as reported in the error, have a look on the sequence entry named `"Mariner-N4_NV"` in your `repbase_all.fasta` file. ...
written 7 weeks ago by nitinnarwade1504200
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Comment: C: Separate column values for summary
... I think this is because you are overwriting the contents of `df` by second file contents, not appending it. To do so you have to store both file contents in separate data frames. ...
written 7 weeks ago by nitinnarwade1504200
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Comment: C: Connect gene names and GO terms after STAR for DESeq2
... As far as I know, DESeq2 will take input in the form of count table like. TranscriptORgeneId Sample1ReadCount Sample2ReadCount SampleNReadCount If you want to directly give genes in DESeq2 input file instead of transcript ids then you can Vlookup GENCODE Transcript Id to their gene name (GTF f ...
written 7 weeks ago by nitinnarwade1504200
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Comment: C: scimpute problem: error in read table
... First thing are you using `GeneCounts_3F-A37B12C16D21.csv` file from `scImpute` package? Second, possible cause as reported in the warning is permission. You just have to change the permission of the folder where you had installed `scImpute` package (If you are using example data from scImpute). Yo ...
written 8 weeks ago by nitinnarwade1504200
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Comment: C: Detection Transposable Elements in eukaryote
... OmicsTools have listed 100+ tools for the same. You can choose one of them appropriate to your work. ...
written 8 weeks ago by nitinnarwade1504200
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Comment: C: How to fetch assembled sequences of different libraries from BAM
... If you have generated Denovo assembly one possible way could be, map raw reads individually on merged assembly using aligner like a` bowtie, bowtie2` etc. It will result in the individual alignment file (.sam; subsequently you can convert it into .bam using `samtools view` utility). Then you can sim ...
written 8 weeks ago by nitinnarwade1504200
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Answer: A: cuffmerge script error
... `cuffmerge` is written in python. if you run it with `./cuffmerge` system will treat cuffmerge as a shell script. You can run it by `python /path/to/cufflink/src/folder/cuffmerge` or you can add it in $PATH variable and call it directly like `cuffmerge` ...
written 8 weeks ago by nitinnarwade1504200
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Comment: C: accessing sequence as columns from file
... Here we have to handle length of line and indexing we can solve it by adding if statement, if(len(line)==i): break else: tempStr += line[i] ...
written 10 weeks ago by nitinnarwade1504200

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