User: vellryba

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vellryba0
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Posts by vellryba

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Comment: C: Is there a way I can upload a reference sequence to Clustal Omega to get alligne
... Sorry to bother you, but do you have any other suggestion? This one wont work due to the reasons below. ...
written 7 weeks ago by vellryba0
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Comment: C: Is there a way I can upload a reference sequence to Clustal Omega to get alligne
... Hi, this only gives me a count at each position. I need to see if they are correlated. Like this: first position 800 second position 1000 count: AT 1000 CT 800 AG 600 etc. ...
written 7 weeks ago by vellryba0 • updated 7 weeks ago by RamRS17k
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Comment: C: Is there a way I can upload a reference sequence to Clustal Omega to get alligne
... Hi, I know there is a mutation present (sometimes) in some of the reads. I also know that there is a mutation (sometimes again) a bit further down the genome. I want to see if that second mutation is only present when the first one is present. In other words, these mutations are hierarchical. I h ...
written 7 weeks ago by vellryba0 • updated 7 weeks ago by RamRS17k
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Comment: C: Is there a way I can upload a reference sequence to Clustal Omega to get alligne
... Hi, I need to know that the mutations came from a single paired read. There are particular regions I have in mind. ...
written 7 weeks ago by vellryba0
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Is there a way I can upload a reference sequence to Clustal Omega to get alligned protein sequences /or a different way of getting the seqeunces
... Hello. My aim is to find out correlated mutations within a single paired reads. For example, I need to know if the sequence ID X, that has mutation at position lets say 800, also has a mutation at position at 1100. So I managed to get bam and sam files containing only reads that span the regions I ...
alignment sequencing written 7 weeks ago by vellryba0
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Comment: C: How to extract just the reads ID, start position and lenght from the alliigned f
... I dont understand how you get a starting position from a sam file. I know in this example: M03972:51:000000000-BJVL8:1:1101:8544:11793 99 gi|11111113|ref|TL| 1058 42 127M = 1129 127 the starting position is 482. How do you get to that? I can the manual, but I thought left most positi ...
written 7 weeks ago by vellryba0
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Comment: C: How to extract just the reads ID, start position and lenght from the alliigned f
... Hi, thank you (couldnt answer till now). So from the example I gave, the starting position should be 482. How do you arrive to that number? Can you explain this to me? This is what I am struggling with. ...
written 7 weeks ago by vellryba0
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Comment: C: How to extract just the reads ID, start position and lenght from the alliigned f
... Its the starting position really. So I have this: M03972:51:000000000-BJVL8:1:1101:8544:11793 99 gi|11111113|ref|TL| 1058 42 127M = 1129 127 I know how to extract M03972:51:000000000-BJVL8:1:1101:8544:11793 and 99. What I dont know is where the alignment starts. Where is the start position? ...
written 7 weeks ago by vellryba0 • updated 7 weeks ago by genomax55k
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Comment: C: How to extract just the reads ID, start position and lenght from the alliigned f
... Well...It has been over two hours since I tried to do this.....This question isnt the first thing I did... I am really not after a lecture. I am after help ...
written 7 weeks ago by vellryba0
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Comment: C: How to extract just the reads ID, start position and lenght from the alliigned f
... I dont normally work with NGS, I just need to to do this one thing. I am extremely short on time. This might loose me days since I am an imposed deadline. Normally, I would agree but this is not my line of work and I am under big pressure to get the preliminary results quickly. ...
written 7 weeks ago by vellryba0

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