Moderator: h.mon

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Posts by h.mon

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Comment: C: What are the most popular sequence alignment and sequence analysis tool/software
... Your question is poorly phrased / thought off. What do you really want to do? From the Bowtie research group, here is a list of tools which may be of interest: - [Crossbow][1] - [Myrna][2] - [CloudBurst][3] - [Contrail][4] A google search for "hadoop next generation sequencing" gave me dozens of ...
written 4 hours ago by h.mon5.7k
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Comment: C: No SNPs in selected sequences and conserved sequences
... Assuming all the unknown details of your experimental set up are correct (good sample size, proper sequencing, possibly known phenotype of the individuals genotyped, etc), even then it would be risky to assume the sequences are conserved. How can you rule out alternative explanations, like a huge ...
written 8 hours ago by h.mon5.7k
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Comment: C: reads clustering of amplicon based sequencing
... It sounds as you may use Qiime or Mothur for what you want, although I am not sure, as your description of the experimental set up and samples is rather fuzzy. What is the size of the amplicon? How did you sequence them? How many samples? Are the samples barcoded or pooled together? ...
written 8 hours ago by h.mon5.7k
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Answer: A: cutadapt loop and paired-end reads
... This is not a bioinformatics question, it is more a shell scripting question. This draft should help you to get started: for i in *_R1.fastq.gz do SAMPLE=$(echo ${i} | sed "s/_R1\.fastq\.gz//") echo ${SAMPLE}_R1.fastq.gz ${SAMPLE}_R2.fastq.gz done ...
written 21 hours ago by h.mon5.7k
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Answer: A: HT-seq count memory error
... Although using featureCounts as genomax suggested is better, if you want to use HTseq, I suggest you sort your sam file by name and set `--order`accordingly. This memory error for position-sorted files is known and old. P.S.: you said which version of Python, but not which version of HTseq. Don't y ...
written 21 hours ago by h.mon5.7k
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Comment: C: Multiple Alignment (~1400 sequences)
... Long time since I used it, but I think for DNA only GTR or CAT (a fast approximation to GTR, for large datasets). There are more option for protein models. ...
written 1 day ago by h.mon5.7k
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Answer: A: SPAdes: <jemalloc>: Error in malloc(): out of memory
... **This is not an answer to your question, but it is very important anyway:** Are you running SPAdes as root? I see it was installed on the `/root/` folder, which is really bad practice. By default, the `/root/` folder permissions are `rwx------ root root`, which means only the root user could acce ...
written 4 days ago by h.mon5.7k
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Comment: C: Picard tools samtofastq for a folder
... Does not work? How it doesn't work? What is the error message? Anyway, I think there should not be spaces after `FASTQ=` and `SECOND_END_FASTQ=`. ...
written 4 days ago by h.mon5.7k
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Comment: C: Any tool designed to align short reads to long reads?
... > How low they are? Get the PacBio version of their reads and look at the error rate on PacBio site. > they have low coverage Pacbio long reads and short reads, want to use > the long reads to link some fragmented repeat contigs. Where do the short reads enter here? Anyway, it seems you ...
written 5 days ago by h.mon5.7k
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Comment: C: Any tool designed to align short reads to long reads?
... PacBio and Nanopore technologies are evolving at a fast pace. Your data is from early or recent iterations? For example, I think recent PacBio has very low error rate and you could use BWA to align short reads onto these long reads. Anyway, what you want to do? If you want to correct long, noisy re ...
written 5 days ago by h.mon5.7k

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