Moderator: genomax

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genomax62k
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Posts by genomax

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Comment: C: how to count the nucleotide frequency of paired ended fasta files
... Official BBMap repo is [located here][1]. Reformat is a versatile utility that does a ton of other things. You can [find a guide here][2]. It is part of a much bigger BBTools package. [1]: https://sourceforge.net/projects/bbmap/ [2]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-gui ...
written 53 minutes ago by genomax62k
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Comment: C: how to count the nucleotide frequency of paired ended fasta files
... > the fastq files are not in this format That is easily fixed using `reformat.sh` from BBMap suite. reformat.sh in=R1.fq.gz out=R1.fa On a serious note you could also look at this: https://digibio.blogspot.com/2017/12/nucleotide-base-frequency-per-read-and.html ...
written 2 hours ago by genomax62k
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Comment: C: Convert BAM files to paired end FASTQ
... Is this TCGA data? You can may be able to use `reformat.sh` from BBMap suite if all you need to do is to reformat the `/1` id's to ones that contain `:`. spaceslash=t Put a space before the slash in addslash mode. addcolon=f Append ' 1:' and ' 2:' to read names, i ...
written 7 hours ago by genomax62k
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Comment: C: Nextseq and Miseq data output difference?
... Major difference is the chemistry. NextSeq uses two color where as MiSeq users 4-color chemistry. Hopefully you have data from NextSeq v.2.5 (or what ever the new chemistry is called). Is it ok to mix sequencing instruments in one analysis .. probably not unless you are able to introduce a batch ef ...
written 7 hours ago by genomax62k
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Comment: C: Automating Trimmomatic for total Noobs
... Advantage of conda is that it does not need root privileges. You can install things in your own home directory. See this guide: https://www.biostars.org/p/335903/ No sudo should be needed. ...
written 1 day ago by genomax62k
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Comment: C: Automating Trimmomatic for total Noobs
... You need to download conda and install into your account on server at school. Then things you install via conda will then live in your personal space on the server. ...
written 1 day ago by genomax62k
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Comment: C: Identification and taxonomic classification of Nematode
... https://www.biostars.org/u/37217/ Use these directions: https://www.biostars.org/p/309884/ ...
written 1 day ago by genomax62k
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Comment: C: Identification and taxonomic classification of Nematode
... Have you looked at "Formatting options" and then under "Other reports" clicked on "Taxonomy report"? You should see something like this. ...
written 1 day ago by genomax62k
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Comment: C: Identification and taxonomic classification of Nematode
... What did you blast against? At NCBI or local? If local, did you get the taxonomy database file, if you downloaded pre-made indexes from NCBI. ...
written 1 day ago by genomax62k
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Comment: C: Portal_client no valid url in the manifest file error
... There are no wrongs. You may want to use imgbb image hosting provider as shown in instructions above in future. I can't see the image you posted above perhaps others can. ...
written 1 day ago by genomax62k

Latest awards to genomax

Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Insert mutations in a reference genome from a vcf
Scholar 6 days ago, created an answer that has been accepted. For C: Insert mutations in a reference genome from a vcf
Commentator 7 days ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Commentator 22 days ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Teacher 23 days ago, created an answer with at least 3 up-votes. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 23 days ago, created an answer that has been accepted. For A: ncbi database update
Scholar 23 days ago, created an answer that has been accepted. For A: ncbi database update
Teacher 26 days ago, created an answer with at least 3 up-votes. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 29 days ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 4 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Have bbduk retain quality scores in output after kmer trimming
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Synthetic DNA/RNA Spike-in standards for NGS
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 5 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 5 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 5 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Scholar 6 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Appreciated 6 weeks ago, created a post with more than 5 votes. For C: Repeat masker bed file
Scholar 6 weeks ago, created an answer that has been accepted. For C: Have bbduk retain quality scores in output after kmer trimming
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For C: Repeat masker bed file
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: merge Fastq or Bam file?

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