User: toralmanvar

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toralmanvar30
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Posts by toralmanvar

<prev • 13 results • page 1 of 2 • next >
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Comment: C: BWA-mem alignment is not giving desired output
... Please check the BWA log messages and see whether BWA was completed normally or with error? This may help you solve your query. ...
written 19 hours ago by toralmanvar30
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Comment: C: sam to bam conversion problem
... [WouterDeCoster][1] means standard log message displayed by BWA got concatenated with your standard .sam output file instead of adding to nohup file. Thus you were able to see BWA log message as first 11 lines of your .sam file. [1]: http://WouterDeCoster I think you should rerun the BWA mem ag ...
written 21 hours ago by toralmanvar30
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Answer: A: sam to bam conversion problem
... you have not mentioned about the parameters you are using for sam to bam conversion, however you can try using simple basic command: samtools view -bS in.sam > out.bam Or you can check out similar post addressing the same issue [here][1] [1]: http://seqanswers.com/forums/showthread.php?t=13 ...
written 1 day ago by toralmanvar30
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Answer: A: making a custom reference
... You can first denovo assemble the reads to generate consensus/contigs and then its can be used as reference to map back reads to it and call SNPs. ...
written 2 days ago by toralmanvar30
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Comment: C: best kmer for genome size estimation
... I don't understand when kmergenie along with best kmer already gives you estimated genome size then why you want to use jellyfish again for the same? Checking the histo.pdf file generated from kmergenie properly can give you required answer. ...
written 4 days ago by toralmanvar30
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Answer: A: Problem with loacting gtf file
... Hello, Looking at the expression file, it seems that you have obtained it after using reference transcriptome pipeline like tophat-cufflinks. Your expression file also have Gene symbols in tracking_id column, which means you have used genome annotation file (.GTF) along with the reference genome fa ...
written 4 days ago by toralmanvar30
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Answer: A: best kmer for genome size estimation
... Hello, You can give a try to [kmergenie][1]. [1]: http://kmergenie.bx.psu.edu/ Mostly it works for me. ...
written 4 days ago by toralmanvar30
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Answer: A: Issue with StringTie to get gene_count matrix for DeSEQ
... Gtf file which you get from stringtie have information for both known and novel transcripts. If 1st column contains Stringtie ID instead of Transcript ID, then that means it represents the novel transcript or isoform which is not of your interest. So after getting gene_count matrix from preDE.py, y ...
written 4 days ago by toralmanvar30
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Comment: C: Where can I get fastq sequence files of length 150 and more.
... Agaz, If transcriptome reads generated from Pacbio interests you then you can access European Nucleotide Archive accession PRJEB3969 (https://www.ebi.ac.uk/ena/data/view/PRJEB3969) ...
written 5 days ago by toralmanvar30
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Answer: A: How to create consensus from bam file without IUPAC code?
... Suresh, Before converting IUPAC ambiguity base symbols to regular bases, I would suggest you to go through the below mentioned post and understand its relation with ploidy. https://www.biostars.org/p/65885/ However, if you are still interested in doing it, then kindly check the weblink: https:// ...
written 5 days ago by toralmanvar30

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