User: k.kathirvel93
k.kathirvel93 • 260
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Posts by k.kathirvel93
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... 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 8 months ago by
k.kathirvel93 • 260
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... 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 8 months ago by
k.kathirvel93 • 260
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5 follow
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... 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 ...
written 8 months ago by
k.kathirvel93 • 260
• updated
8 months ago by
manojkumarbioinfo • 60
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... 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 ...
written 8 months ago by
k.kathirvel93 • 260
• updated
8 months ago by
Anand Rao • 350
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... 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 8 months ago by
k.kathirvel93 • 260
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... 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 ...
written 8 months ago by
k.kathirvel93 • 260
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... 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 ...
written 9 months ago by
k.kathirvel93 • 260
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... I tried a lot, but always end up with problems. Thanks ...
written 9 months ago by
k.kathirvel93 • 260
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... 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 9 months ago by
k.kathirvel93 • 260
0
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... @cpad0112 Can you help with this thread? ...
written 9 months ago by
k.kathirvel93 • 260
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