Date: Fri, 29 Mar 2024 16:16:08 +0100 (CET) Message-ID: <1336420330.2885.1711725368139@localhost> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_2884_732101094.1711725368137" ------=_Part_2884_732101094.1711725368137 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html
Hello,
I am trying to look at some of the actual reads that mapped to a p= articular gene using the GEUVADIS data set.
For example, lets say I have a bed file for one individual (SAMPLE1.bed)= and the gencode annotation file (GENCODE.v12.gtf). I would like the output= to be bed file oriented like this:
Mappedread_ID Mappedrea= d_Chr Mappedread_start &nb= sp; Mappedread_end = Mappedread_sequence G= ene_ID Gene_chromosome &nbs= p; Gene_start = Gene_end
HWI-ST:XXXXX 1 &= nbsp; = 15000  = ; 15020  = ; &nb= sp; ATTTATATGATTTATATAT ENSG0000012= 34 Chr 1 &nbs= p; 14000 &nbs= p; 16000 &nb= sp;
With my limited understanding about flux-capacitor, it seems to me that = its main purpose is to generate read counts for each gene and does not retu= rn the actual read ID's which mapped to a certain gene.
I managed to do this in bedtools by using the following command, but was= n't sure if bedtools and flux-capacitor are operating in the same fashion.<= /p>
bedtools intersect -a SAMPLE1.bed -b GENCODE.v12.gtf -wb > output.txt=
Is the equivalent to the above possible using flux capacitor ?
Thanks,
Jin