User: ppurkayastha2010

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Posts by ppurkayastha2010

<prev • 15 results • page 1 of 2 • next >
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How to export the SNPs between whole genome alignments using the command line?
... I am using Mauve to align two the whole genome sequences, one of the sequence is in the form of contigs. Another one is in the form of a complete genome. I could align the two sequences using the following command progressiveMauve ref.fa contigs.fa --output alignment.xmfa And to extract the S ...
command-line variants mauve snp alignment written 12 weeks ago by ppurkayastha201030 • updated 12 weeks ago by Jennifer Hillman Jackson25k
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Dot plot between two sequences
... Hi All, Is there any tool to plot dot plot between two sequences such that each sequence will lie in an axis. X axis- sequence 1 and Y axis -sequence 2. And dots are the matching genes between the two sequences. ...
alignment assembly written 3 months ago by ppurkayastha201030 • updated 3 months ago by Hotz, Hans-Rudolf1.8k
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Pileup file using NCBI-SRA toolkit
... I have a pileup format file for a particular accession SRR1011475. This pileup format file was obtained using NCBI sratoolkit. MT_H37RV_BRD_V5 750 C 1 ^~, # MT_H37RV_BRD_V5 751 C 1 , # MT_H37RV_BRD_V5 752 G 1 , # MT_H37RV_BRD_V5 753 C 1 , # MT_H37RV_BRD_V5 754 G 1 , # But I ...
galaxy pileup sratoolkit ngs written 7 months ago by ppurkayastha201030 • updated 7 months ago by Jennifer Hillman Jackson25k
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Comment: C: Unable to download larger files more than a GB
... I couldn't find any solution from the previous post since i posted the question in comment section. In order to have a solution for my question, I have created a new post for this. ...
written 7 months ago by ppurkayastha201030
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(Closed) Unable to download larger files more than a GB
... I am trying to download a data-set consisting of 50 bam files, I use the following command to download $ wget https://usegalaxy.org/api/dataset_collections/d20ad3e1ccd4595de/download?key=MYSECRETAPIKEY but I am unable to download the data beyond 1 GB. I tried to download using Curl, but I still ...
bam collection usegalaxy.org api download written 7 months ago by ppurkayastha201030 • updated 7 months ago by Jennifer Hillman Jackson25k
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Comment: C: How to download a batch consisting of 50 bam files, using CURL or wget
... but this is not allowing to download more than a GB data. Showing an error **Read error at byte 1079804844 (Success).Retrying.** ...
written 7 months ago by ppurkayastha201030
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Comment: C: How to download a batch consisting of 50 bam files, using CURL or wget
... Thanks a lot :-) I could download the files now.. ...
written 7 months ago by ppurkayastha201030
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How to download a batch consisting of 50 bam files, using CURL or wget
... How could I download a batch consists of 50 bam files, using CURL or wget. I tried the following solution, https://biostar.usegalaxy.org/p/26527/ but still is not working :( wget -O --no-check-certificate 'https://usegalaxy.org/api/dataset_collections/d103ecff2e1c7b62/download' --2018- ...
wget galaxy linux curl written 7 months ago by ppurkayastha201030 • updated 7 months ago by Martin Čech ♦♦ 4.9k
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How do I process multiple pileup files at once with Varscan to get the vcf files?
... I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN. VARSCAN takes an input in pileup format. I could get the pileup files for all 100 SRAs using **NCBI SRA Tools**. But not able to give the List of pileup files to Varscan, in order to generate VCF files. Is there a ...
pileup varscan snp sra written 8 months ago by ppurkayastha201030 • updated 8 months ago by Jennifer Hillman Jackson25k
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De-novo assembly of a bacterial genome
... I am trying to assemble a bacterial genome of length 8Mb in **orione.crs4.it** . I could successfully load the paired-end illumina dataset into the server, but I am unable to do the de-novo assembly for the paired end data using any of the programs. Could anyone suggest if the tools are working in ...
orione.crs4.it bacterial genome denovo assembly written 18 months ago by ppurkayastha201030 • updated 18 months ago by Jennifer Hillman Jackson25k

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