User: biolab

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biolab890
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Posts by biolab

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Comment: C: Is it OK to use --split-files option in fastq-dump when processing SE data?
... OK, genomax, thanks a lot for your explanations. I will try EBI-ENA. ...
written 17 days ago by biolab890
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Comment: C: Is it OK to use --split-files option in fastq-dump when processing SE data?
... Hi, genomax, could you please tell me the safe usage of fastq-dump? Thank you very much! ...
written 18 days ago by biolab890
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Comment: C: Is it OK to use --split-files option in fastq-dump when processing SE data?
... Thanks a lot, Devon Ryan. ...
written 18 days ago by biolab890
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Is it OK to use --split-files option in fastq-dump when processing SE data?
... Hi, everyone, I have a list of SRR accessions and need to process them using Fastq-dump. Some of them are SE, and others are PE data. Do you think it OK to use `--split-files` option in fastq-dump when processing SE data? I want to use one fastq-dump command to process both SE and PE data (my c ...
fastq-dump written 18 days ago by biolab890 • updated 18 days ago by Devon Ryan68k
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Comment: C: How to download raw data in batch from NCBI based on Series Accession number or
... Hi, Buffo, thanks for your comment! However, after uploading a list of Platform ID (eg, GPL19657), I could not get the SAR run number, which is something like SRR4024915. ...
written 4 weeks ago by biolab890
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Comment: C: How to download raw data in batch from NCBI based on Series Accession number or
... Thank you for your comment, genomax! The GEO Series Accession Number is something like GSE65022, and the Platform ID is like GPL19657. I want to get the SRA number something like SRR4024915. ...
written 4 weeks ago by biolab890
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How to download raw data in batch from NCBI based on Series Accession number or Platform ID
... Dear all, I have a list of NCBI GEO Series Accession numbers and Platform IDs, and want to download the raw data in batch. A previous post on Biostars presents a good example of batch download (https://www.biostars.org/p/111040/ ), but that solution is based on project ID rather than GEO Series A ...
sra written 4 weeks ago by biolab890 • updated 4 weeks ago by genomax29k
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Comment: C: Removing shorter reads in PE mapping
... Thanks a lot, genomax2. ...
written 6 weeks ago by biolab890
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Comment: C: Removing shorter reads in PE mapping
... Thanks a lot Brian. It's very helpful. I will try that. ...
written 6 weeks ago by biolab890
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Comment: C: Removing shorter reads in PE mapping
... Thank you very much, Brian. So, do you think one way is to do separate mapping for R1 and R2? Thanks! ...
written 6 weeks ago by biolab890

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