User: Paul

gravatar for Paul
Paul40
Reputation:
40
Status:
New User
Location:
India
Last seen:
1 day, 8 hours ago
Joined:
5 years, 11 months ago
Email:
p***************@gmail.com

Posts by Paul

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Mapping multiple reads to a single genome
... oh! can I generate a single bam file for all the subfolders? will that be fine? In that case, I can put all the SRR files in a single folder and map it against a single reference sequence. But I have thousands of SRR files ...
written 3 days ago by Paul40
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Mapping multiple reads to a single genome
... I have a number of pair-end and single-end reads to map it to a reference genome. TaxonID SRR files 1448592 SRR1172918 SRR1175065 SRR1184297 SRR1196515 1448462 SRR1180190 SRR1181352 SRR1181404 SRR1183042 1402586 SRR1011524 SRR1019194 1448524 SRR1172749 SRR1173120 SRR1184340 ...
bash written 3 days ago by Paul40 • updated 3 days ago by PoGibas4.6k
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Comment: C: Is there a way to download FASTq files from SRR IDs?
... Thank you @genomax EBI-ENA. worked well in my case :) ...
written 10 days ago by Paul40
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Is there a way to download FASTq files from SRR IDs?
... I have a bunch of SRR IDs and need to download Fastq files for the same. I tried downloading SRAtoolkit for the same by doing apt-get install sra-toolkit export PATH=$PATH:$PWD/sratoolkit.2.8.2-1-ubuntu64/bin which fastq-dump /User/sratoolkit.2.8.2-1-ubuntu64/bin/fastq-dump fa ...
sra eutility fastq written 11 days ago by Paul40 • updated 11 days ago by h.mon8.0k
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Answer: A: Retrieving SRA files using Taxonomic IDs
... I got my answer by doing this `$ esearch -db sra -query "txid1448409[Organism:noexp]" | efetch -format runinfo | cut -d ',' -f 1 | grep SRR` ...
written 11 days ago by Paul40 • updated 11 days ago by genomax32k
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Comment: C: Retrieving SRA files using Taxonomic IDs
... Thanks. So, the xmls need to get parsed for taxonomy_sra IDs?? ...
written 11 days ago by Paul40
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Retrieving SRA files using Taxonomic IDs
... I have a list of taxonomic IDs with genomic IDs as shown below: Taxon ID Genome ID 1438833 1438833.3 1438845 1438845.3 1438847 1438847.3 Is there a way to retrieve SRA files using the above mentioned taxon IDs or Genome IDs?? ...
sra eutility taxonomy written 11 days ago by Paul40
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Comment: C: Error in fetching the Refseq using Taxonomic ID
... Thanks :) it worked like a charm ...
written 15 days ago by Paul40
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Comment: C: Error in fetching the Refseq using Taxonomic ID
... Thanks it's not showing error anymore. But results in multiple sequences, whereas I need only one RefSeq sequence (NC_000962.3) ...
written 16 days ago by Paul40
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Comment: C: Error in fetching the Refseq using Taxonomic ID
... but there is only one reference sequence (NC_000962.3) with respect to taxonomic ID "txid1438843[Organism]" https://www.ncbi.nlm.nih.gov/genome/?term=txid1438843+%5BOrganism%5D ...
written 16 days ago by Paul40

Latest awards to Paul

Scholar 11 days ago, created an answer that has been accepted. For A: Retrieving SRA files using Taxonomic IDs
Supporter 3 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For Mapping HGNC ID to uniprot ID

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