User: toralmanvar

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toralmanvar290
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Posts by toralmanvar

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Answer: A: Align Reads from PacBio
... You can align your pacbio data with 'bbmap **mapPacBio.sh**' or 'bwa **mem**' to reference gene sequence. However, mapPacBio can very well handle raw PacBio reads with high error rates. Have a look at this [previous post][1]. [1]: https://www.biostars.org/p/231559/ ...
written 1 hour ago by toralmanvar290
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Answer: A: QIIME filter_fasta.py not removing chimeric sequences
... Like masta|511 said, please make sure that you are using chimeric.txt file as input. Also chimeric txt header file should not start with ">" symbol. Otherwise, the command which you are using is correct, but again looking at your fasta sequence IDs, I feel you have not run "split_library.fastq.p ...
written 2 days ago by toralmanvar290
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Comment: C: Combining Maker and Blast2Go
... I properly checked my Penicillium blast2GO file, and result was as follows: - Total genes : 11.2 k - Without hits : 70 - With blast hits : 5.8 k - With mapping : 40 - With GO annotation : 5.2 k Means from total of 11.k NR annotated data, 5.2 k genes were mapped and GO annotated also. ...
written 2 days ago by toralmanvar290
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Answer: A: stringTie Warning message
... You are using GFF annotation file while running strintie, but it is always better to use GTF file. Stringtie has issued a warning as there are overlapping segments in your GFF file. > Here, GFF warning: "merging adjacent/overlapping segments of > Cotton_A_18708_BGI-A2_v1.0 on chr1 (28601099- ...
written 3 days ago by toralmanvar290
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Answer: A: How do you use BLAST?
... We usually use blast/blast for identification of sequences or comparing sequences or for orienting sequences based on reference. Mostly we use it for annotation purpose using publicly available databases. Filtering of blast result is usually based on query coverage, alignment length, mismatch or se ...
written 3 days ago by toralmanvar290
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Comment: C: Combining Maker and Blast2Go
... You have got GOs for ~50% of your genes, which I don't find low. This is very much accepted number. I have worked on, one of the species of Penicillium and has got very similar results to yours. But there, I have not used 'maker' for gene prediction instead I had used GeneMark-ES. And if I remember ...
written 4 days ago by toralmanvar290
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Comment: C: How to improve fastq quality based on fastqc output ?
... First, you need to clarify what you have sequenced using NGS platform and second, what is the aim of your project. Because all these parameters need to tackle carefully based on your requirement. For instance, RNASeq data have high duplication rate, amplicon sequencing can have abnormal GC content e ...
written 4 days ago by toralmanvar290
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Answer: A: BLAST+ error: No alias or index file found for nucleotide database
... TBLASTN search translated nucleotide databases using a protein query, but in your case I can see that you have prepared protein database using -dbtype 'prot' instead of nucleotide database using 'nucl'. Thus please make sure to use protein sequences as query and database should be nucleotide sequenc ...
written 4 days ago by toralmanvar290
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Answer: A: counting after aligning miRNA reads to miRBase mature miRNA instead of reference
... yes, you can map the reads to mature miRNAs and can count the reads mapping onto it using samtools idxstat. Alternatively use can try using tool like mirdeep2 for complete analysis of miRNAs. ...
written 4 days ago by toralmanvar290
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Comment: C: Combining Maker and Blast2Go
... Can you please give us more detail like, whether you are using blast2GO or blast2GOPro? Suggest you to try blastP of few protein sequences online/standalone and upload the resulting .xml file in blast2GOpro. If this works, then surely there is problem at blast level. ...
written 4 days ago by toralmanvar290

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Teacher 5 days 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 4 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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