User: toralmanvar

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toralmanvar530
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Posts by toralmanvar

<prev • 111 results • page 1 of 12 • next >
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Comment: C: RNA-seq : Quantification problem after mapped with BBMap
... please list some header of sequences and screenshot of gtf file to give us better idea. ...
written 7 weeks ago by toralmanvar530
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Answer: A: where to download RNA-SeQC_v1.1.8.jar file from?
... You can download it from [here][1]. [1]: https://software.broadinstitute.org/cancer/cga/rnaseqc_download ...
written 7 weeks ago by toralmanvar530
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Comment: C: Get all the nucleotides from a bam file that is aligning to specific position in
... Its strange. And why 3rd column which represents reference base is "N"?. What is the actual reference nucleotide in that position? I suggest you to give it a try again considering the broad region (~5000k). ...
written 8 weeks ago by toralmanvar530
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Comment: C: Using Circos plot to visualize RNA-seq data
... hello badredda, but you have not attached the image properly. Please refer [this][1] post for adding image to biostar post. [1]: https://www.biostars.org/p/309884/ ...
written 8 weeks ago by toralmanvar530
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Comment: C: Removing N's from NextSeq reads
... Ok, I have never worked on scRNAseq so didn't know this. ...
written 8 weeks ago by toralmanvar530
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Answer: A: Removing N's from NextSeq reads
... You can download [prinseq][1] and can use prinseq-lite.pl script in it to remove sequences containing desired number of "Ns". You can use parameter command having following paramters: prinseq-lite.pl -fastq test_R1.fastq -fastq2 test_R2.fastq -ns_max_n (number of 'N') > I've received my se ...
written 8 weeks ago by toralmanvar530
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Answer: A: How to design degenerative primer in R?
... You can try using [hyden][1], [iCODEHOP][2] or [genefisher2][3] . For more options you can check out [this][4] post of research gate. [1]: http://acgt.cs.tau.ac.il/hyden/ [2]: https://www.bitnos.com/info/icodehop [3]: https://bibiserv2.cebitec.uni-bielefeld.de/genefisher2 [4]: https://www. ...
written 8 weeks ago by toralmanvar530
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Answer: A: Get all the nucleotides from a bam file that is aligning to specific position in
... If you mean, you want to extract read base which is aligning to particular position of your genome, then you can try [samtools mpileup][1] or [gatk Pileup][2]. You can explore more about mpileup format [here][3]. Samtools mpileup will give you output in form of 5 columns : - Sequence identifier - ...
written 8 weeks ago by toralmanvar530
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Comment: C: How to extract reads belonging to sense intron/exon and antisense intron/exon wh
... hello genomax, can you tell me the reason why you think that it is the similar post to my previous post? ...
written 8 weeks ago by toralmanvar530
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Answer: A: Software for Taxonomic Profiling of Fungi
... Use can also use KAIJU webserver, where you can upload combined/stitched ITS reads and can choose "NCBI BLAST nr +euk" (It includes eukaryotes along with fungi and microbial eukaryotes) as reference database to consider. It is sensitive and still very fast. Alternatively you can download and install ...
written 8 weeks ago by toralmanvar530

Latest awards to toralmanvar

Scholar 5 weeks ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file
Supporter 8 weeks ago, voted at least 25 times.
Teacher 8 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
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Teacher 4 months 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 8 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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