User: biolab

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biolab860
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Posts by biolab

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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 3 days ago by biolab860
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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 3 days ago by biolab860
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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 days ago by biolab860 • updated 4 days ago by genomax27k
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Comment: C: Removing shorter reads in PE mapping
... Thanks a lot, genomax2. ...
written 14 days ago by biolab860
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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 14 days ago by biolab860
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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 15 days ago by biolab860
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Comment: C: Removing shorter reads in PE mapping
... Thank you very much for your answer. The command I used is: `cutadapt -a SEQ --trim-n -o out.fq in.fq`, I used a perl script to remove reads < 18-nt. Can I ask a further question? Although the pairing information is lost as you mentioned, are the mapping positions of reads correct? To me, th ...
written 15 days ago by biolab860
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Removing shorter reads in PE mapping
... Dear all, I have pair-end (PE) sequencing data (R1.fq and R2.fq). First, I removed the adapters, which resulted in unequal sequence length for some PE reads. Then I removed the reads with length < 18-nt, which resulted in different number of reads for the R1.fq and R2.fq data. Do you think it ...
mapping written 15 days ago by biolab860 • updated 15 days ago by h.mon5.7k
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Comment: C: Which tool was used to generate this mapping file?
... Thank you, Brian. I am re-doing mapping. I agree to start from beginning. ...
written 4 weeks ago by biolab860
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Comment: C: Which tool was used to generate this type of mapping file?
... Honestly, the file was from my friend's friend. The reads are short RNA sequences mapped on MIR gene locus. The actual size of the reads are relatively longer. I just make an example there. ...
written 4 weeks ago by biolab860

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