User: nitinnarwade1504

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Posts by nitinnarwade1504

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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 8 days ago by nitinnarwade1504170
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Comment: C: Running two bedtools commands in series produces error "has non positional recor
... you can try something like this. bedtools intersect -a A.vcf -b B.vcf | bedtools subtract -a stdin -b C.vcf ...
written 8 days ago by nitinnarwade1504170
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Comment: C: DE seq analysis using transcript expression data
... first of all, you should have a raw read count table for each of your samples i.e. control as well as treatment. To prepare raw read count table you have to map your raw reads on the reference genome. If your doing Denovo assembly (i.e. Reference genome is not available for an organism) then you hav ...
written 8 days ago by nitinnarwade1504170
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Comment: C: Excel column filer using Perl
... So basically you want to manipulate excel file (`.xlsx`) in Perl? If yes there are very nice sample codes given on metacpan. xlsx xls and as zx8754 said how is it related to Bioinformatics? ...
written 9 days ago by nitinnarwade1504170
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Comment: C: How to get the all the overlap information of a peak in ChIPseeker
... overlap-of-peaks-and-annotated-genes section given in ChIPseeker manual may help you. ...
written 9 days ago by nitinnarwade1504170
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Comment: C: Eigensoft - smartpca - error line 65
... Can you please post command used for running smartpca? ...
written 9 days ago by nitinnarwade1504170
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Comment: C: DNA barcode sequences for Qiime2 and meaning of it
... 1. Actually, barcodes are needed when your running multiple samples in one run of sequencing. These index sequences/barcode sequences used to identify which read is coming from which sample. 2. Generally, barcode sequences will be in the header of your .fastq file. The last segment of few nucleoti ...
written 9 days ago by nitinnarwade1504170
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Comment: C: SSRs abundance calculation
... Do you want the abundance of repeat sequence or abundance of mono, di, tri, tetra etc repeats (not sequences just length of repeat)? If you are interested in the abundance of the length of repeats then it's pretty simple. There is one column `SSR type` in which `p1` means mono-nucleotide repeat `p2 ...
written 9 days ago by nitinnarwade1504170
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Comment: C: Fastq file from SRA database not mapping to to the genome
... What was the error? Can please post it. ...
written 9 days ago by nitinnarwade1504170
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Comment: C: accessing sequence as columns from file
... Hello mdsiddra, Have you checked indentation for that line? ...
written 9 days ago by nitinnarwade1504170

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