User: mks002

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mks002150
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http://www.manishkumar...
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Posts by mks002

<prev • 75 results • page 1 of 8 • next >
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Comment: C: MAKER command maker2zff .ann and .dna files are empty
... You can try alternate method . Use the following command To merge the gff maker/bin/gff3_merge -d Bcon_rnd1_master_datastore_index.log -o bcon_genome.all.gff -g To get the protein sequences and then transcripts sequences Maker/maker/bin/fasta_merge -d Bcon_rnd1_master_datastore_index.log ...
written 26 days ago by mks002150
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DELLY SNV detection output intrepetation
... Dear all, I have performed SNV calling on plasmodium samples. However I am facing some difficulty to interpreting certain fields. I wish to annotate this .vcf file further. Here is an example from one of the .vcf file Pf3D7_02_v3 903199 BND00000329 A A]Pf3D7_01_v3:84434] . ...
genome snp delly snv written 8 weeks ago by mks002150
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Comment: C: Trimmomatic SureSelect protocol
... Do one thing run [FastQC][1] on your fastq files and check for the over represented sequences. If any such adapter is present in your sample , you ll get to know after ruuning fastqc. Good luck [1]: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ...
written 9 weeks ago by mks002150
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Comment: C: Trimmomatic SureSelect protocol
... Use some ten bases "CTGTCTCT" and go ahead for trimming. Below is the text from Manual: MiSeq platform sequencing run setup and adaptor trimming guidelines Use the Illumina Experiment Manager (IEM) software to generate a custom primer Sample Sheet. Set up the run to include adapter trimming using ...
written 10 weeks ago by mks002150
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Comment: C: Trimmomatic SureSelect protocol
... can u share the top 10 lines of fastq files`head "input.fastq"` ...
written 10 weeks ago by mks002150
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Comment: C: Trimmomatic SureSelect protocol
... I think you are first time working with NGS data. You have to convert the SRA sequences to fastq format using [fastq-dump][1]. Then on the fastq files you can perform trimming. you start reading more post on biostar to get yourself going. [1]: https://www.biostars.org/p/109276/ ...
written 10 weeks ago by mks002150
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Comment: C: Scope for improvements in a whole Genome Assembly
... Hello [Vijay Lakhujani][1], can u detail what improvement approaches are there. [1]: https://www.biostars.org/u/26377/ ...
written 11 weeks ago by mks002150
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Comment: C: Merging multiple sets of transcripts (generated by Trinity)
... yes correct cd-hit is based on similarity and some other threshold. >Cluster 7 0 30057aa, >Oar_XP_011987898.1... * 1 30057aa, >Oar_XP_011987907.1... at 1:30057:1:30057/99.95% >Cluster 8 0 30008aa, >Oar_XP_011987916.1... * >Cluster 9 0 ...
written 11 weeks ago by mks002150
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Comment: C: Merging multiple sets of transcripts (generated by Trinity)
... Hello liorglic Merging or "clustering" of fasta files i think u have mentioned above . Read the following thread [CD-HIT][1]. Hope this serves your purpose. [1]: https://www.biostars.org/p/108519/ ...
written 11 weeks ago by mks002150
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Comment: C: Gene ontology in sheep
... use the link below from Kegg server https://www.genome.jp/kegg-bin/get_htext?htext=oas00001&filedir=%2fkegg%2fbrite%2foas&length= U can download the information as htext. ...
written 11 weeks ago by mks002150

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