Admin: GenoMax

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GenoMax94k
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Posts by GenoMax

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Comment: C: Bulk RNAseq data for COVID-19 with patient metadata?
... Take a look at this resource: https://outbreak.info/ In any case, patient metadata is unlikely to be available publicly due to privacy reasons. ...
written 2 hours ago by GenoMax94k
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Answer: A: What types of acc. no. exist?
... This is a [good summary][1] of all GenBank accession numbers. UniProt accession numbers are described [at this link][2]. `5YFE` is a PDB ID. These databases cross-reference data where possible to facilitate linking information together. [1]: https://community.gep.wustl.edu/repository/course_mate ...
written 6 hours ago by GenoMax94k
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Comment: C: sortmerna terminates without generating the file with rRNA being removed
... I have moved a comment (that was able to keep the flow of the thought process) to an answer. You can accept it providing closure to this thread. ...
written 6 hours ago by GenoMax94k
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Comment: C: Human contamination in Chimpanzee or Bonobo data
... > I know tools such as Kraken can be used to identify contamination Likely not useful when species are so closely related. Do you have your own sequence data for the species you mention? Take a look at `RemoveHuman.sh` from BBMap suite which is described [in this thread][1]. It is going to be ...
written 7 hours ago by GenoMax94k
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Comment: C: K-mer sequencing vs sequence-alignment
... Introduction sections for the papers have cross-references that you will likely find useful. `hash` ([LINK][1]) describes the original technique for large scale-sequence comparisons. > we even can use k-mer sequencing for determining whether two strings are similar or not. Not sure what you ex ...
written 8 hours ago by GenoMax94k
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Comment: C: K-mer sequencing vs sequence-alignment
... Guess you have not looked at links for the two papers I posted in my comment above. ...
written 9 hours ago by GenoMax94k
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Comment: C: K-mer sequencing vs sequence-alignment
... If you intend to identify genes then using this toy example is inappropriate. One would need to use much longer k-mers. [This paper][1] may help provide some background reference materials. [One more][2] tool. [1]: https://www.frontiersin.org/articles/10.3389/fmicb.2020.02067/full [2]: https:/ ...
written 22 hours ago by GenoMax94k
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Comment: C: Issue when merging FastQ
... I am not sure what aligner you are using. Perhaps it is paying attention to fastq headers and having `R2` headers show up in `R1 files may be an issue for it. > I was thinking that by doing cat file1_R1.gz file1_R2.gz > outfil1.gz > , tthen map this file and then by removing duplicates it ...
written 1 day ago by GenoMax94k
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Comment: C: Issue when merging FastQ
... > have been merging 2 paired-end fastq files using Just to be sure, you are merging `R1` and `R2` files independently and in the same order e.g. `cat file1_R1.gz file2_R1.gz ..` and `cat file1_R2.gz file2_R2.gz ..`? You can't do `cat file1_R1.gz file1_R2.gz`. ...
written 1 day ago by GenoMax94k
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Comment: C: Which adapters to use for trimming?
... This is NOT the official BBTools repository. Official BBMap distribution is located at [SourceForge][1]. Once you download and extract BBMap (from official repo), `resources` directory will be inside the uncompressed BBMap folder. [1]: https://sourceforge.net/projects/bbmap/ ...
written 2 days ago by GenoMax94k

Latest awards to GenoMax

Scholar 5 hours ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: how to combine RNA seq data from 4 lanes
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Scholar 4 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For C: How to analyze Illumina RNASeq data
Scholar 5 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
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Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Bowtie2 and hisat2 indexes
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
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Scholar 6 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
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Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Linearize fasta files
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Scholar 9 days ago, created an answer that has been accepted. For A: Identify FASTQ files containing multiple DNA sequences based on specific sequen
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