User: toralmanvar

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toralmanvar420
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Posts by toralmanvar

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Comment: C: hisat2 was not worked
... check [this][1] link. Though it has no relevance with hisat2, but it do have with Mac OS. [1]: https://github.com/yousseb/meld/issues/62 ...
written 21 hours ago by toralmanvar420
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(Closed) How to extract reads belonging to sense intron/exon and antisense intron/exon while working with small RNA sequence
... I have Illumina data of 1 x50bp from small RNA library. I am interested in identifying known and novel miRNAs in my plant, whose reference genome is not available. However, first I want to count the reads aligning Exon sense, Exon antisense, Intron sense, Intron antisense. Basically, I want to repli ...
srna exon sense exon antisense intron sense written 21 hours ago by toralmanvar420
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Comment: C: Trim Paired-end Fastq Files
... This may sound stupid, but can you tell us how you have count the reads? Because if you are simply using grep command with "@" symbol then it may end-up counting sequence header as well as qualities in fourth line of sequence (i.e in illumina, 31 quality value is represented by symbol "@") which re ...
written 1 day ago by toralmanvar420
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Answer: A: GATK errors with RealignerTargetCreator and IndelRealignment
... for solving this error : > ERROR StatusLogger Unable to create class > org.apache.logging.log4j.core.impl.Log4jContextFactory specified in > jar:file:/home/as/RNAP/GenomeAnalysisTK.jar!/META-INF/log4j-provider.properties > ERROR StatusLogger Log4j2 could not find a logging implementati ...
written 8 days ago by toralmanvar420
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Comment: C: Extracting reads belonging to different RNA families from Rfam
... Actually I want to classify the ncRNAs like the table shown ![here][1]. [1]: https://image.ibb.co/hFiq48/ncRNAs.png ...
written 8 days ago by toralmanvar420
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Answer: A: How I can find flanking regions
... You can use [seqkit subseq][1] with -d (for downstream seq) and -u (for upstream sequence) option or "--only-flank" option to get only up/down stream sequence based on your requirement. [1]: https://bioinf.shenwei.me/seqkit/usage/#subseq ...
written 9 days ago by toralmanvar420
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Answer: A: How I can find sequences
... If you have bed/gff file of coordinates, then you can use [bedtools getfasta][1] and if you have just couple of coordinates to extract the you can try [seqkit faidx][2] which is similar to samtools faidx [1]: http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html [2]: https://bio ...
written 10 days ago by toralmanvar420
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Answer: A: bam-readcount and paired end data
... I think better approach would be to first call the SNP from BAM file using software like samtools or GATK. VCF file thus generated after calling SNP posses the information of number of reads representing your reference and alternate allele along with many more important information. ...
written 10 days ago by toralmanvar420
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Answer: A: SSRs abundance calculation
... When you run misa.pl on your scaffold file, two files are generated: 1. .misa file 2. .statistics file So you can get different types of repeats along with the times they appeared in .statistics file ...
written 10 days ago by toralmanvar420
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Answer: A: DNA barcode sequences for Qiime2 and meaning of it
... DNA barcode used in metagenome sequencing is not for species identification, instead it is for distinguishing different samples run together in single sequencing run through the process of multiplexing. Means during library preparation, different barcodes (unique 6-8bp sequence) are added to each sa ...
written 11 days ago by toralmanvar420

Latest awards to toralmanvar

Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to extract specific rows based on row number from a file
Scholar 6 months ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file

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