table problem with GTF file

Question

[roberta.cracco]

Hello. I'm facing some issues on filtering a GTF file. Every filter I try to apply dont produce any results and I think it is because of this:

Long story short, one of the filters I tried was in R, and the first time I tried to open the GTF file, i got a warning that line 714 did not have XX elemtns, so I added a Fill = True, and this is the result

I guess this formating problem is the reason why i cant filter this file. I have a TCONS list with several ids and neither grep, awk nor the filter in R are working... Here it is the pipes i`m trying:

grep –f result_cpc2_15m_clean.txt /short_path/merged_asm/merged.gtf.class_code_15m | cut -c 1- > outgrep.merged_15m.gtf 

awk -F'"' 'FNR==NR {block[$0];next} $2 in block' result_cpc2_15m_clean.txt /media/disk4/gopec/cracco/lncRNA/15m/merged_asm/merged.gtf.class_code_15m > outgrep.merged_15m.gtf

Does anyone now if this is the problem and how can i fix it? Im a newbie and know almost nothing on bioinfo

Thanks in advance

PS: forgot to mention that taking a more careful look, it seems these lines (714, 716, 721) have an extra "contained_in" column, right before the "nearest_ref" column. Also, this file was filtered by classcodes (x, u and j)

[Pierre Lindenbaum]

grep –f result_cpc2_15m_clean.txt what's n this file

cut -c 1- why this ?

awk -F'"' 'FNR==NR {block[$0];next} $2 in block' what is that awk script ?

it would be easier if you could describe what's your final aim with this GTF ?

[roberta.cracco]

Hi!! result_cpc2_15m_clean.txt is the file where I have all my ids i want to filter the gtf file for. This GTF file will be used as input on cuffdiff for differential expression analysis.

This IDs are lncRNA and i want to test their differential expression between my groups