User: germelcar

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germelcar10
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10
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New User
Location:
Mexico/Ensenada/CICESE
Last seen:
1 month ago
Joined:
8 months, 1 week ago
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g********@gmail.com

Posts by germelcar

<prev • 27 results • page 1 of 3 • next >
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Comment: C: hash function for DNA sequences
... Hello Devon. Could you please share what the hash compression function do you use in order to assign and index for the hash value returned by murmur? What size of the hash table do you use? Thanks in advance. ...
written 5 weeks ago by germelcar10
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Comment: C: Is There A Fast Hashing Function For Nucleotide K-Mers (Q-Grams)?
... What hash compression technique do you use for the hash values returned by lookup3/8? How do you determine the hashtable size? Thanks in advance. ...
written 5 weeks ago by germelcar10
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Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
... Thanks for the reply. ...
written 10 weeks ago by germelcar10
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Answer: A: The Biostar Handbook. A bioinformatics e-book for beginners.
... Is correct to try to cite the handbook? If yes, how would I cite it? BWT, what about de novo transcriptome assembly? Would be great to include a section for that. For fastq-dump, I see that the Handbook uses version 2.5.2. I remember a notice from SRA-Toolkit's github page saying that one should u ...
written 10 weeks ago by germelcar10
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Comment: C: Weird base qualities and sequences from FastQ file?
... Thanks. I will try trimmomatic and also BBMap as @genomax2 has suggested me. Many thanks for the help. ...
written 4 months ago by germelcar10
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Comment: C: Weird base qualities and sequences from FastQ file?
... Thanks for your help. The authors say the following about the filtering process about the reads: > 70 bp paired-end reads were prepared for assembly by Q15 filtering, > removal of library adapter sequences, removal of A/T stretches and > short reads (less than 60 bp). The percent of rejec ...
written 4 months ago by germelcar10
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Comment: C: Weird base qualities and sequences from FastQ file?
... Hi WouterDeCoster, thanks for your reply. I will put a copy in verbatim of the "library preparation and Illumina sequencing" section of the paper: > The quality of total RNA was checked using a NanoDrop 2000 (Thermo > Fisher, USA) and an Agilent 2100 Bioana- lyzer (Agilent, USA). The RNA > ...
written 4 months ago by germelcar10
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Comment: C: Weird base qualities and sequences from FastQ file?
... Hi **mastal511**, thanks for your reply. I do not know what do you mean by older sequencing data, how new sequencing data look like? I have understood that the data was sequenced using HiSeq 2000, which I have understood is not too old. Do you recommend me to use the reads without a processing/fil ...
written 4 months ago by germelcar10
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Weird base qualities and sequences from FastQ file?
... Hi everyone: I have some difficulties, it is new and weird for me and I need some help with recommendations/advices. I realize that the fastq files have a lot lot of reads with qualities marked as "#" and the bases are marked as "N" for the entire read, and in some other reads, the bases are maked ...
assembly fastq next-gen rna-seq written 4 months ago by germelcar10 • updated 4 months ago by mastal5111.6k
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Comment: C: Tophat Library-Type : Illumina Truseq Stranded Total Rna Sample Prep Kit
... Could you please share the Zhao Zhang's title paper? Thanks in advance. ...
written 5 months ago by germelcar10

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