User: toralmanvar

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toralmanvar90
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Posts by toralmanvar

<prev • 31 results • page 1 of 4 • next >
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Comment: C: SSPACE-LongRead, PBjelly2 and OPERA-LG comparison
... Hello, have you got answer to this question from anywhere? I am also trying to analyse same type of data and want to know which tool can give better result. ...
written 6 weeks ago by toralmanvar90
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Comment: C: How to align genomes on Mauve
... If you are using genbank file then try using fasta file too. ...
written 6 weeks ago by toralmanvar90
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Comment: C: run htesq-count error
... Request you to check the version of python you are using as it can be a probable reason for this error. Please check HTSeq documentation, mentioning its [Prequisites and installation][1]. Similar HTSeq issue is been discussed in one of [chinese blog][2] [1]: https://htseq.readthedocs.io/en/rele ...
written 6 weeks ago by toralmanvar90
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Answer: A: How to align genomes on Mauve
... Similar issue is already discussed in [sourceforge thread][1]. Hopefull it will help resolving the error. [1]: https://sourceforge.net/p/mauve/mailman/message/32283745/ ...
written 7 weeks ago by toralmanvar90
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Comment: C: HOw to modify the description line 1 of a fastaq file to match with third line?
... To replace SRR1188607.1 from the begining, you can use: sed "s/SRR1188607.1@HWI-ST915/@HWI-ST915/g" in_file.fastq >out_file.fastq Here SRR1188607.1@HWI-ST915 part will be substituted by @HWI-ST915 in your first header line. ...
written 7 weeks ago by toralmanvar90
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Answer: A: quality filtering error usearch
... Suggest you to check the fastq statistics after using cutadapt. If in case, whole sequence gets trimmed due to presence of adapter sequence, cutadapt does not remove the header, instead it leaves header with an empty sequence line. So it is always advisable to run cutadapt with minimum length cri ...
written 7 weeks ago by toralmanvar90
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Answer: A: HOw to modify the description line 1 of a fastaq file to match with third line?
... To remove anything after '+' from 3rd line, you can use simple sed one liner: sed "s/+SRR1188607.*/+/g" in_file.fastq >out_file.fastq ...
written 7 weeks ago by toralmanvar90 • updated 7 weeks ago by genomax42k
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Answer: A: denovo assembly combining multiple data sets
... SOAPdenovo2 is a good choice. You can also try velvet and newbler which gives you option of considering reference genome as input and provides reference guided assembly ...
written 7 weeks ago by toralmanvar90
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Answer: A: velvetg failed during the assembly
... Couple of months back, I also encountered the same error and I didnt get any solution. Similar issue is posted on velvet github issue page but there is no answer to it. However, when I used older version of velvet (precisely 1.1.07), it solved my problem. So you can also use your velveth result as ...
written 7 weeks ago by toralmanvar90
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Answer: A: Error in TRinity
... SRR1188607 is a paired-end data so you should get 2 files after converting .sra file to fastq. If this is not the case, then please rerun fastqdump. Command which I use for PE data is : fastq-dump -I --split-files input_file.sra Give a try. ...
written 7 weeks ago by toralmanvar90 • updated 7 weeks ago by genomax42k

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Scholar 8 weeks ago, created an answer that has been accepted. For A: how to get the strand from a blast xml file

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