Moderator: genomax

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genomax40k
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Posts by genomax

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Comment: C: How to cont fasta sequences efficiently using (or not ) biopython
... > How to cont fasta Count/concatenate/check length? ...
written 8 hours ago by genomax40k
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Comment: C: Trimmomatic job script to run on multiple pair end read file
... That is correct. Replace the part that is common to all files. I am going to assume that the `fa.gz` above is an error. Trimmomatic will expect `fastq format files as input. ...
written 8 hours ago by genomax40k
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Comment: C: Trimmomatic job script to run on multiple pair end read file
... https://www.biostars.org/p/237119/#237130 ...
written 10 hours ago by genomax40k
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Answer: A: Trimmomatic job script to run on multiple pair end read file
... One way to do this. for i in `ls -1 *R1*.fastq | sed 's/\_R1.fastq//'`; do echo trimmomatic PE -phred33 $i\_R1.fastq $i\_R2.fastq $i\_R1_paired.fq.gz $i\_R1_unpaired.fq.gz $i\_R2_paired.fq.gz $i\_R2_unpaired.fq.gz ILLUMINACLIP:contams_forward_rev.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4: ...
written 10 hours ago by genomax40k
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Comment: C: RNA-seq Bacterial Alignments Using NCBI Database
... If you can get away with using `nr` or [refseq bacteria][1] then you could look into [DIAMOND][2]. Aligning against 100s of bacterial genomes would not be a trivial thing.Especially if you plan to use a "regular" NGS aligner. [1]: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria/ [2]: https: ...
written 12 hours ago by genomax40k
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Comment: C: what does the result show in Hisat ?
... You are right. We had already discussed this in other thread: https://www.biostars.org/p/293875/#293889 ...
written 13 hours ago by genomax40k
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Comment: C: Sringtie gff output has "STRG." instead of genid
... See this: https://www.biostars.org/p/259259/#259320 ...
written 14 hours ago by genomax40k
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Comment: C: Alignment of protein domains with MDAT: Any suggestions?
... Take a look at the README.md file included in the distribution. It says this: > Certain data is need by MDAT. For it to be found automatically you > need to copy the content of the folder data into a (hidden) folder in > your home named ".mdat". Alternatively you can give the domain math & ...
written 15 hours ago by genomax40k
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Comment: C: low mappability in single cell rna-seq data?
... One should never trim reads independently (if you have paired end data). You are also not scanning/removing Illumina adapters. ...
written 15 hours ago by genomax40k
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Comment: A: Question: Looking for a microbial metabarcoding course
... https://www.biostars.org/p/292646/ Same folks have done a microbial one in past: https://www.biostars.org/p/238982/ No personal experience. Linking relevant thread for reference. ...
written 16 hours ago by genomax40k

Latest awards to genomax

Appreciated 14 hours ago, created a post with more than 5 votes. For NovaSeq from Illumina (updated info)
Teacher 1 day ago, created an answer with at least 3 up-votes. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Scholar 14 days ago, created an answer that has been accepted. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Teacher 15 days ago, created an answer with at least 3 up-votes. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Scholar 15 days ago, created an answer that has been accepted. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Teacher 21 days ago, created an answer with at least 3 up-votes. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Scholar 21 days ago, created an answer that has been accepted. For C: How to remove reads from fastq flle that match to a set of reads in my fasta fil
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Suggestions regarding bioinformatics journal
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Why "Motile sperm domain-containing protein 2" has nothing to do with "sperm"?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Scholar 5 weeks ago, created an answer that has been accepted. For A: Genome annotation of mouse that only includes long non coding RNa
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Professor assign me some tasks, gene ontology sucks. Anyone please guide me, i a
Scholar 6 weeks ago, created an answer that has been accepted. For A: Genome annotation of mouse that only includes long non coding RNa
Scholar 6 weeks ago, created an answer that has been accepted. For A: Genome annotation of mouse that only includes long non coding RNa
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Professor assign me some tasks, gene ontology sucks. Anyone please guide me, i a
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Why "Motile sperm domain-containing protein 2" has nothing to do with "sperm"?
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: Why "Motile sperm domain-containing protein 2" has nothing to do with "sperm"?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Genome annotation of mouse that only includes long non coding RNa
Scholar 7 weeks ago, created an answer that has been accepted. For C: Help downloading pepper genome (I have bad speed connection)
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: over presented kmer in fastq

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