User: 2nelly

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2nelly150
Reputation:
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Athens
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1 day, 1 hour ago
Joined:
3 years, 2 months ago
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Posts by 2nelly

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Faster way to run macs14
... No, but you always have the option to split the analysis per chromosome ...
written 2 days ago by 2nelly150
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Comment: C: fastq file format error
... **cpad0112** That is more elegant of course. Good job ...
written 7 days ago by 2nelly150
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Comment: C: fastq file format error
... You can restore your fastq file using the code below. I split the commands in a step by step pipe so you can easily see what every command is doing. I am not sure if the FFFFFFFs you get are base quality from sequencer or alignment quality. But in any case this will not affect the realignment. ...
written 7 days ago by 2nelly150
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Answer: A: Whole Exome CNV tools
... Hi BAGeno, I would suggest you to use VarScan, which is designed specifically for the type of data you have (WES). [Somatic Copy Number Alteration (CNA) Calling][1] [1]: http://varscan.sourceforge.net/copy-number-calling.html Cheers! ...
written 11 weeks ago by 2nelly150
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Comment: C: SRA submission Error
... my bad!! sorry for that ...
written 4 months ago by 2nelly150
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Comment: C: SRA submission Error
... The error should probably be due to the same name. First be sure that the name are different. For example in biosample add sample only once (no replicates) Then at the end add an ID column like in metadata. The in metadata, for every sample you can upload different replicates like i told you ( filen ...
written 4 months ago by 2nelly150 • updated 4 months ago by RamRS21k
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Comment: C: SRA submission Error
... First of all, you should put sample name only once (e.g. MN1806CN_treatment_Aphid_30d). Then at the end of the file (excel or txt) there are columns like Filename filename2 filename3. This is where you put your full fastq name : MN1806CN_treatment_Aphid_30d_R1.fastq MN1806CN_treatment_Aphid ...
written 4 months ago by 2nelly150 • updated 4 months ago by RamRS21k
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Comment: C: Using GATK4 Mutect2 on mouse data, need a genome snp reference
... if your goal is to discard germline variants, I would suggest to annotate the Mutect2 output for dbsnp (or file of your interest) using a tool like snpSift and then filter them out. However, you can always go back to GATK3 in which parameter dbsnp is active ...
written 5 months ago by 2nelly150
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Comment: C: scan DNA sequence for known motifs
... You guys keep adding noise to threads, by accusing me for not providing the correct query info. Seems like it is easy to you to criticize people behind your keyboard instead of trying to get a second look at the question. I think it s pointless to look for any solution in this thread. P.S. The dm ...
written 5 months ago by 2nelly150
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Comment: C: scan DNA sequence for known motifs
... Dear ATpoint, I already have the occurrences of some candidate motifs, came from thousands regions. What I am looking for is to check if this motif is found in a db like jaspar. Thank you ...
written 5 months ago by 2nelly150

Latest awards to 2nelly

Popular Question 8 months ago, created a question with more than 1,000 views. For ADTEx coverage issue
Popular Question 11 months ago, created a question with more than 1,000 views. For ADTEx coverage issue
Popular Question 11 months ago, created a question with more than 1,000 views. For Control-FREEC breakPointThreshold value
Popular Question 13 months ago, created a question with more than 1,000 views. For Control-FREEC breakPointThreshold value
Popular Question 16 months ago, created a question with more than 1,000 views. For Control-FREEC error message
Popular Question 20 months ago, created a question with more than 1,000 views. For Control-FREEC error message
Popular Question 23 months ago, created a question with more than 1,000 views. For mutation signature in cancer

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