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User: k.kathirvel93

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k.kathirvel93 • 260
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India
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2 months, 3 weeks ago
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Posts by k.kathirvel93

<prev • 170 results • page 1 of 17 • next >
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Comment: C: How to remove sequence reads contains more than 1 X from multifasta file?
... Thanks for the advice. > Here you asked how to remove sequences containing N characters ? Still i didn't get any solution for this, which is why i came up with a new thread. i tried with googlong also, but i couldn't get any. If i am better in scripting i could've done by myself. Taking ideas ...
written 3 months ago by k.kathirvel93 • 260
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Comment: C: How to remove sequence reads contains more than 1 X from multifasta file?
... Hi Mr. Pierre Lindenbaum, Thanks for the fast reply, your awk script is removing fine reads( with no X) also. can you help again. and also i made few changes on my question, can you help with this modified thread ? ...
written 3 months ago by k.kathirvel93 • 260
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How to remove sequence reads contains more than 1 X from multifasta file?
... I have 5000 protein sequences in one multifasta file. I found more reads have gaps as X in their reads. So, want to eliminate those reads completely (Whole protein seq) from the file. I am keeping filter criteria as if a read contains morethan 2 X ( continuesly or anywhere in the read) should be rem ...
sequence sequencing written 3 months ago by k.kathirvel93 • 260 • updated 3 months ago by manojkumarbioinfo • 60
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Phylogenetic tree construction from MAFFT aligned large genome dataset ?
... Hi EveryOne, I have MSA file of 11000 genomes (30k size each) aligned by MAFFT. I want to construct a phylogenetic tree from this large MSA file (500megabytes). I tried MEGAX and RAxML but, it takes so long and at last it got crashed in my ubuntu 16.04, 8GB RAM and 1TB HD workstation. So, can anyon ...
genome alignment sequence written 3 months ago by k.kathirvel93 • 260 • updated 3 months ago by Anand Rao • 310
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Comment: C: how to remove specific sequences from multi-fasta file which contains N ?
... Thanks @Pierre Lindenbaum, I have gone through that thread you mentioned, but it was not working fine with my large data, coz after executed that code, still the genome have Ns. Since that thread was 4 yrs old, i created my own thread. Can you help with this? Thanks ...
written 3 months ago by k.kathirvel93 • 260
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how to remove specific sequences from multi-fasta file which contains N ?
... Hi EveryOne, I have a multifasta file which contains 11000 (30kb each) genomes. Now i want to remove all the reads(whole genome) which contains N (minimum atleast one N ). How can I do this with sed or awk? Thanks in advance. I have input like this : >Genome1 ATCGTCGTACAGATACAGATACANNNcGATAGAC ...
genome sequence alignment sequencing written 3 months ago by k.kathirvel93 • 260
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extract only reads repeated more than 10 times from BLASTp excel sheet output
... Hi EveryOne, I have BLASTp output which contains 8 columns, the 3rd column contains repeated aminiacid sequences one cell by one cell. Now i want to extract only reads which is repeated more than 10 times in 3rd column (along with other 7 columns). thanks. Sorry for not giving any examples, because ...
assembly sequence alignment written 3 months ago by k.kathirvel93 • 260
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Comment: C: How to perform BLASTp with two multifasta protein sequence files?
... I tried a lot, but always end up with problems. Thanks ...
written 4 months ago by k.kathirvel93 • 260
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Comment: C: How to extract sequences from multi fasta file, which contains specific primers?
... Thanks @cpad0112, by the mistake you have taken both my input and expected output in one single file and you filtered the expected output sequence alone. but clearly.... Input reads are like M01015:63:000000000-D2M18:1:1102:14195:28796 GGCACTCGTATCGATGCGGCCGCGGTAAACTCCACCCGGAGCAAGGCCAAATAGGGGTTCAT ...
written 4 months ago by k.kathirvel93 • 260
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Comment: C: How to extract sequences from multi fasta file, which contains specific primers?
... @cpad0112 Can you help with this thread? ...
written 4 months ago by k.kathirvel93 • 260

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