User: ppurkayastha2010

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Posts by ppurkayastha2010

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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 9 days ago by ppurkayastha201020 • updated 8 days ago by Jennifer Hillman Jackson24k
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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 11 days ago by ppurkayastha201020
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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 17 days ago by ppurkayastha201020 • updated 16 days ago by Jennifer Hillman Jackson24k
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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 17 days ago by ppurkayastha201020
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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 17 days ago by ppurkayastha201020
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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 18 days ago by ppurkayastha201020 • updated 17 days ago by Martin Čech ♦♦ 4.5k
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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 5 weeks ago by ppurkayastha201020 • updated 5 weeks ago by Jennifer Hillman Jackson24k
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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 11 months ago by ppurkayastha201020 • updated 11 months ago by Jennifer Hillman Jackson24k
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Aligning more than 2 sequences
... I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end reads with two reference sequences. I need to align the 3 sequences (pair end file, reference1, and reference 2) in such a way that in a bam file, I can see these three aligned and mapped to each othe ...
variant analysis alignment ngs written 12 months ago by ppurkayastha201020 • updated 12 months ago by Jennifer Hillman Jackson24k
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How to filter SNP and Indel data
... I have mapped my sequence with a wild type sequence using Bowtie2 and obtained around 8000 SNPs and 700 Indels using Varscan. Please let me know how do I further shortlist the SNPs and Indels (based on which criteria)? The output file looks like this POS #CHROM ID REF ALT QUAL FILTER INFO FORM ...
variant analysis snp indels written 12 months ago by ppurkayastha201020 • updated 12 months ago by Guy Reeves1.0k

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