Get gene counts from *.sam file and annotation

Question

[tim.ivanov.92]

I have a list of alignment (.sam/.bam formats) from RNAseq experiment and i want to get gene counts from them. The problem is that these alignments have chromosomes as reference, not genes:

NB501288_407_HGYJKBGX7:1:11101:22149:1027#GAGATTGTCAGT  0       chr8    141541926       37      70M     *       0       0       ATTTCNTATGACATTGGGTTCTCATACAGGTCTGCAGTTCAAAATCCAAGTTTGAAATCTGGGACGGAAG  AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE  XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:5C64
NB501288_407_HGYJKBGX7:1:11101:6394:1028#GAGATTGTCAGT   0       chr1    33790402        37      70M     *       0       0       GTCTGNCTGGCTCTGCTCAGTCGGGAGGAGGCGCCCTGGGCCAGAATCCTGGCTGCCACCAGCCCTAGGA  AAAAA#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEE/EEAEEEEEEEE/  XT:A:U  NM:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:5T64
NB501288_407_HGYJKBGX7:1:11101:19502:1031#GAGATTGTCAGT  16      chr2    97474290        25      70M     *       0       0       CCCCTCCGACCGTTCCCCAGCACACCCCACCCCACTCAGCCGCTCAGCCTCCCTCAGTTACCCANACCGC  <EEEEEEAEAEEEEEEEEEAE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE#AAAAA  XT:A:U  NM:i:4  X0:i:1  X1:i:0  XM:i:4  XO:i:0  XG:i:0  MD:Z:3T0G1A57G5

Is there a tool from samtools package to intersect them with gtf annotation to get gene counts, not chromosome?

[GenoMax]

featureCounts and htseq-count are standard software programs to get gene counts from SAM/BAM files.

[tim.ivanov.92]

thats not really solving my problem, i first need to use something like bedtools intersect

[reza.jabal]

To get the gene counts you need to annotate your aligned reads first (based on the coordinates in the 3rd and the 4th column!)

[tim.ivanov.92]

yeah, thats what my goal is the beast i've found so far is bedtools intersect

[reza.jabal]

You are on track!

1) Download a bed file containing the coordinates of all Gencode genes (You can download it from the UCSC table browser).

2) Convert your bam to bed:

samtools view -bq 20 -F 1796 "XXX.bam" | bamToBed -i stdin >  XXX.bed

3) In bedtools run:

bedtools intersect -a XXX.bed -b Genes.bed  -wa  >  intersect.bed

4) Get the total number of overlapped baits:

wc -l  intersect.bed