User: michael.ante

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michael.ante3.2k
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Posts by michael.ante

<prev • 352 results • page 1 of 36 • next >
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Comment: C: Is there a tool that filters a sam/bam file by the following: (1) similarity sco
... I don't know any tool that can do that automatically. I guess the easiest way is to parse each alignment with the softclips in the CIGAR string for the length fraction and the MD-tag for the similarity. If your BAM file is encoded in sam1.4, you can just use the CIGAR string. If you want to compar ...
written 4 days ago by michael.ante3.2k
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Comment: C: col as names
... You can use in the read.table command the parameter `skip=1` ...
written 6 days ago by michael.ante3.2k
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Answer: C: Inconsistent number Pandaseq vs grep
... Fastq read ids should not start with a `>` but rather with a `@`. You are maybe counting the occurrences of the quality score encoded by `>`. [Edit] Fastq files can be counted by `wc -l my.fastq | awk '{print $1/4}` , since fastq files have a defined structure. Each read is described by 4 l ...
written 6 days ago by michael.ante3.2k
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Comment: C: Htseq-count result assistance
... Check your alignment stats. While aligning RNA-SEQ data to all patches, haplotype annotations you might get a lot of multi-mapping reads which will not be counted with default Htseq-count settings. ...
written 6 days ago by michael.ante3.2k
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Comment: C: col as names
... Can you show us the result of `head -n 3 gene_tpm.txt | cut -f 1-3` from the command line? ...
written 6 days ago by michael.ante3.2k
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Comment: C: col as names
... Does the first row of your file starts with a '#' ? While testing on an example (R3.4.4), this lead to skipping the first line. Do you want to have you rownames as colnames? ...
written 6 days ago by michael.ante3.2k
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Answer: A: Htseq-count result assistance
... Hi citynsukka, The genes with a read count greater than 0 are MT-genes. Please check if your GTF is consistent with your reference used. Use `head` to get the chromosome names out of yor GTF file and `samtools view -H` to get the names out of your bam file. Cheers, Michael ...
written 6 days ago by michael.ante3.2k
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Comment: C: Bowtie Index building for wheat genome
... Try `bowtie2-inspect wheat.fasta.bowtie > my_bowtie.fa` and compare the output to your `wheat.fasta` file. ...
written 12 days ago by michael.ante3.2k
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Comment: C: Bowtie Index building for wheat genome
... Hi, the wheat genome may be too big due to its chromosomes' length exceeding the size allocated for storing it, see e.g. [https://www.biostars.org/p/12560/][1]. You can generate a STAR index, but you'll need a lot of RAM (>= 126GB). [1]: https://www.biostars.org/p/12560/ ...
written 12 days ago by michael.ante3.2k
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Comment: C: STAR fusion error
... Try to avoid spaces in file/folder names or use the appropriated comment function (like `/home/app/Desktop/Untitled\ Folder/`) ...
written 12 days ago by michael.ante3.2k

Latest awards to michael.ante

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
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Scholar 3 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
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Scholar 12 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Scholar 15 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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