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Hi
I have 2 files which are tab delimited.
file1
chr1 5 10 P1 KR4
chr1 10 20 1H LA1 R0 TA1
file2
P1 G6 13.27 0.2425
P1 KR4 18.79 0.3060
P1 DND1 19.44 0.2833
N1 DH1 0.99 1.08
1H R0 0.9 NA...

Hii
Thank you very much. I have another problem what if only first 2 fields are identical are rest are not
for example:
I feel nothing as usual
I feel something unusual

still i want to get ...

I have an input file like this...
All iI want to do is If the lines are identical except for the last field i want to merge them into single line
input_file
I feel something is nothing
I feel...

Hi, this is what i am calling as overlap

F1: |-----|
F2: |-----|

F1: |-----|
F2: |--|

F1: |-----|
F2: |-----|

F1: |-----|
F2: |---------|

ya the overlap happens with neighbor lines only

we have to check for overlaps based on 2nd and 3rd column

in file1 first line 2nd and 3rd columns are 22 and 25. in file2 the first line contains 24 and 25. i,e., we have to check ...

use piping
head -2 abc >a |cp a 123

In file1 and we have to check for the overlpping regions based on column 2 and 3. and if overlapps are found whole lines have to be printed. the lines of first file followed by the lines of second...

I have two files that contain overlapping positions. i want to put them together each overlapping entries in both files in to a new file (the entries of first file first and the entries of second...

hi akshay
If i use your code on this data set
chr11 87578121 87579121 chr11 87578115 87579115 ID1
chr11 87578193 87579193 chr11 87578115 ...

hi
its giving output something like this:

chr15 99874874 99875874 chr15 99875173 99876173 aa1
chr15 99874962 99875962 chr15 99875173 ...

I have file like this:
chr start end
chr15 99874874 99875874 chr15 99875173 99876173 aa1
chr15 99874923 99875923 chr15 99875173 99876173 aa1...

input
Id1 chr9 fox12_exon_0_F chr9 56 72 72660772 H3K4ME2_E 726 72 promoter intergenic_Nedd4_exon_0_Foutput
Id1 chr9 fox12 chr9 56 72 72660772 ...

for entries like this filed1 field2 gene_intron_24_R ...filed10 field11 gene_intron_24_ it is just replacing only those that occur after field2. it is not replacing after field11. I should have been...

I have tried awk '{sub("_intron_\.[0-9]+\.[A-Z]", "")}1' file |awk '{sub("_exon_\.[0-9]+\.[A-Z]", "")}1'

but unfortunately for intergenic its not doing anythg

Hi
I have a file like that contains infomation about genes exons introns made as a single string. i am just planning to get the gene name alone with out any extra information. ...

Hey sorry its a mistake i edited it

I have a file like this

AFF3 BCL2
AGTRAP BRAF
AHRR NCOA2
AKAP9 BRAF
And second input file like this

chromosome start end gene
chr1 38177326 38664955 AFF3...

Thank you for your suggestions i got it working

I have a file that contains 2 columns tag,pos
cat input_file

tag pos
atg 10
ata 16
agt 15
agg 19
atg 17
agg 14
I have used following command to sort the file based on second column
sort...

Thats exactly what i needed

I made it in .xls format so that the fields would be clearly seperated from each other. please see to it

There are many isoforms so tissue field may not be identical even if they have same gene name. I want all (only if we consider gene names they appear to be duplicates but when we see other fields...

I have attached the file and sent. It seems that requires moderators permission so soon i think it will be approved and you can see to it

I need all the three fields separated by tab but when i am applying for my huge data somehow it is mixing everything so i thought i would copy each column separately into new file